Uncovering the growing burden of enteric fever: A molecular analysis of Salmonella Typhi antimicrobial resistance

Enteric fever, a persistent public health challenge in developing regions, is exacerbated by suboptimal socioeconomic conditions, contaminated water and food sources, and insufficient sanitation. This study delves into the antimicrobial susceptibility of Salmonella Typhi, uncovering the genetic underpinnings of its resistance. Analyzing 897 suspected cases, we identified a significant prevalence of typhoid fever, predominantly in males (58.3 %) and younger demographics. Alarmingly, our data reveals an escalation in resistance to both primary and secondary antibiotics, with cases of multi-drug resistant (MDR) and extensively drug-resistant (XDR) S. Typhi reaching 14.7 % and 43.4 %, respectively, in 2021. The Multiple Antibiotic Resistance (MAR) index exceeded 0.2 in over half of the isolates, signaling widespread antibiotic misuse. The study discerned 47 unique antibiotic resistance patterns and pinpointed carbapenem and macrolide antibiotics as the remaining effective treatments against XDR strains, underlining the critical need to preserve these drugs for severe cases. Molecular examinations identified blaTEM, blaSHV, and blaCTX-M genes in ceftriaxone-resistant strains, while qnrS was specific to ciprofloxacin-resistant variants. Notably, all examined strains exhibited a singular mutation in the gyrA gene, maintaining wild-type gyrB and parC genes. The erm(B) gene emerged as the primary determinant of azithromycin resistance. Furthermore, a distressing increase in resistance genes was observed over three years, with erm(B), blaTEM and qnrS showing significant upward trends. These findings are a clarion call for robust antimicrobial stewardship programs to curtail inappropriate antibiotic use and forestall the burgeoning threat of antibiotic resistance in S. Typhi.

In vitro susceptibility of ceftolozane/tazobactam against typhoidal, non-typhoidal and extended spectrum β-lactamase-producing Salmonella

Both typhoidal and non-typhoidal salmonellae are included in the top 15 drug-resistant threats described by the Center for Disease Control and Prevention of the United States. There is an urgent need to look for alternative antibiotics for the treatment of Salmonella infections. We examined the in vitro susceptibilities of ceftolozane/tazobactam and six other antibiotics on typhoidal and non-typhoidal salmonellae, including isolates that are extended-spectrum β-lactamase (ESBL)-positive, using the broth microdilution test. Of the 313 (52 typhoidal and 261 non-typhoidal) Salmonella isolates tested, 98.7% were susceptible to ceftolozane/tazobactam. Based on the overall MIC_50/90 values, Salmonella isolates were more susceptible to ceftolozane/tazobactam (0.25/0.5 mg/L) compared to all other comparator agents: ampicillin (≥64/≥64 mg/L), levofloxacin (0.25/1 mg/L), azithromycin (4/16 mg/L), ceftriaxone (≤0.25/4 mg/L), chloramphenicol (8/≥64 mg/L) and trimethoprim/sulfamethoxazole (1/≥8 mg/L). When comparing the activity of the antimicrobial agents against non-typhoidal Salmonella isolates according to their serogroup, ceftolozane/tazobactam had the highest activity (100%) against Salmonella serogroups D, G, I and Q isolates, whereas the lowest activity (85.7%) was observed against serogroup E isolates. All the 10 ESBL-producing Salmonella (all non-typhoidal) isolates, of which 8 were CTX-M-55-producers and 2 were CTX-M-65-producers, were sensitive to ceftolozane/tazobactam albeit with a higher MIC_50/90 value (1/2 mg/L) than non-ESBL-producers (0.25/0.5 mg/L). In summary, our data indicate that ceftolozane/tazobactam is active against most strains of both typhoidal and non-typhoidal salmonellae and also active against ESBL-producing salmonellae.

Emergence of ceftriaxone resistant Salmonella enterica serovar Typhi in Eastern India

In view of widespread isolation of fluoroquinolone (FQ) resistant Salmonella enterica serovar Typhi globally, third generation cephalosporins (ceftriaxone) are used as alternative drugs for treatment of typhoid fever in recent years. But reports on emergence of third generation cephalosporin resistant S. Typhi have been documented from various countries including India posing threat in future use of this drug for typhoid treatment. Here, we report on genomic analysis of a third generation cephalosporin resistant S. Typhi strain isolated for the first time from Eastern India, Kolkata during 2019. The study strain was phenotypically resistant to ceftriaxone, ampicillin. Whole genome sequencing revealed the presence of conjugative IncX3 plasmid carrying bla_SHV-12 gene on it. The study strain belongs to H58 haplotype (4.3.1.2) and ST1 type. Comparison of phylogenetic analysis of the study strain with other cephalosporin resistant S. Typhi strains across the world revealed that three strains isolated from Western part of India during 2016 were its closest neighbours. Hence close monitoring of cephalosporin resistant S. Typhi strains are of great importance to control the furure use of this antibiotic for the treatment of typhoid fever.

Advancement in Salmonella Detection Methods: From Conventional to Electrochemical-Based Sensing Detection

Large-scale food-borne outbreaks caused by Salmonella are rarely seen nowadays, thanks to the advanced nature of the medical system. However, small, localised outbreaks in certain regions still exist and could possess a huge threat to the public health if eradication measure is not initiated. This review discusses the progress of Salmonella detection approaches covering their basic principles, characteristics, applications, and performances. Conventional Salmonella detection is usually performed using a culture-based method, which is time-consuming, labour intensive, and unsuitable for on-site testing and high-throughput analysis. To date, there are many detection methods with a unique detection system available for Salmonella detection utilising immunological-based techniques, molecular-based techniques, mass spectrometry, spectroscopy, optical phenotyping, and biosensor methods. The electrochemical biosensor has growing interest in Salmonella detection mainly due to its excellent sensitivity, rapidity, and portability. The use of a highly specific bioreceptor, such as aptamers, and the application of nanomaterials are contributing factors to these excellent characteristics. Furthermore, insight on the types of biorecognition elements, the principles of electrochemical transduction elements, and the miniaturisation potential of electrochemical biosensors are discussed.

Prevalence of Salmonella enterica serovar Typhi infection, its associated factors and antimicrobial susceptibility patterns among febrile patients at Adare general hospital, Hawassa, southern Ethiopia

BACKGROUND

Salmonellas enterica serovar Typhi (S.typhi) causes typhoid fever and is a global health problem, especially in developing countries like Ethiopia. But there is a little information about prevalence and factors association with S.typhi and its antimicrobial susceptibility pattern in Ethiopia especially in the study area. The aim of this study was to determine the prevalence of S.typhi infection, its associated factors and antimicrobial susceptibility pattern among patient with a febrile illness at Adare General Hospital, Hawassa, Southern Ethiopia.

METHODS

Hospital based cross sectional study was conducted among 422 febrile patients from May 23, 2018 to October 20, 2018. A 5 ml venous blood was collected from each febrile patient. Culture and biochemical test were performed for each isolate. Antimicrobial susceptibility testing was performed for each isolate using modified Kirby-Bauer disk diffusion techniques.

RESULT

In this study, the prevalence of S.typhi among febrile illness patients at Adare General Hospital was 1.6% [95% confidence interval (CI): 0.5-2.9]. The age of the study subjects were ranged from 15 to 65 years (mean age 32 years). It was observed that participants who came from rural area had 8 times (AOR 8.27: 95% CI: 1.33, 51.55) more likely to had S. typhi infection when compared with urban dwellers. The microbial susceptibility testing revealed that all six of S.typhi isolates showed sensitive to Ceftriaxone and all 6 isolates showed resistant to nalidixic acid and Cefotaxime and 5(83.3%) susceptible to Chloramphenicol and Ciprofloxaciline. Multidrug resistance (resistance to three or more antibiotics) was observed among most of the isolates.

CONCLUSION

S. typhi bacteraemia is an uncommon but important cause of febrile illness in our study population. Ceftriaxone therapy is a suitable empirical antibiotic for those that are unwell and suspected of having this illness. Further surveillance is required to monitor possible hanging antibiotic resistant patterns in Ethiopia.

Drug-resistant enteric fever worldwide, 1990 to 2018: a systematic review and meta-analysis

BACKGROUND

Antimicrobial resistance (AMR) is an increasing threat to global health. There are > 14 million cases of enteric fever every year and > 135,000 deaths. The disease is primarily controlled by antimicrobial treatment, but this is becoming increasingly difficult due to AMR. Our objectives were to assess the prevalence and geographic distribution of AMR in Salmonella enterica serovars Typhi and Paratyphi A infections globally, to evaluate the extent of the problem, and to facilitate the creation of geospatial maps of AMR prevalence to help targeted public health intervention.

METHODS

We performed a systematic review of the literature by searching seven databases for studies published between 1990 and 2018. We recategorised isolates to allow the analysis of fluoroquinolone resistance trends over the study period. The prevalence of multidrug resistance (MDR) and fluoroquinolone non-susceptibility (FQNS) in individual studies was illustrated by forest plots, and a random effects meta-analysis was performed, stratified by Global Burden of Disease (GBD) region and 5-year time period. Heterogeneity was assessed using the I2 statistics. We present a descriptive analysis of ceftriaxone and azithromycin resistance.

FINDINGS

We identified 4557 articles, of which 384, comprising 124,347 isolates (94,616 S. Typhi and 29,731 S. Paratyphi A) met the pre-specified inclusion criteria. The majority (276/384; 72%) of studies were from South Asia; 40 (10%) articles were identified from Sub-Saharan Africa. With the exception of MDR S. Typhi in South Asia, which declined between 1990 and 2018, and MDR S. Paratyphi A, which remained at low levels, resistance trends worsened for all antimicrobials in all regions. We identified several data gaps in Africa and the Middle East. Incomplete reporting of antimicrobial susceptibility testing (AST) and lack of quality assurance were identified.

INTERPRETATION

Drug-resistant enteric fever is widespread in low- and middle-income countries, and the situation is worsening. It is essential that public health and clinical measures, which include improvements in water quality and sanitation, the deployment of S. Typhi vaccination, and an informed choice of treatment are implemented. However, there is no licenced vaccine for S. Paratyphi A. The standardised reporting of AST data and rollout of external quality control assessment are urgently needed to facilitate evidence-based policy and practice.

TRIAL REGISTRATION

PROSPERO CRD42018029432.

Prevalence and antimicrobial susceptibility pattern of Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi among febrile patients at Karamara Hospital, Jigjiga, eastern Ethiopia

Objective:

The aim of this study was to determine the prevalence and antimicrobial susceptibility pattern of Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi among febrile patients at Karamara Hospital, Jigjiga, eastern Ethiopia.

Methods:

A cross-sectional study was conducted among 203 febrile patients presumptive of enteric fever (Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi) at Karamara Hospital from 15 February to 20 March 2016. Venous blood was collected, cultured, and biochemical tests were performed. Antimicrobial susceptibility testing was performed for each isolate using modified Kirby–Bauer disk diffusion technique.

Results:

The overall prevalence of enteric fever (Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi) was 11%. The prevalence of Salmonella enterica serovar Typhi (7%) was higher than Salmonella enterica serovar Paratyphi (4%). The odds of having enteric fever were higher among the study participants aged 31–45 years and with previous history of enteric fever. Most of the Salmonella enterica serovar Typhi isolates were sensitive to tetracycline (78.6%), gentamycin (64.3%), and ceftriaxone (64%), while most of the isolates of Salmonella enterica serovar Paratyphi were sensitive to tetracycline (100%), gentamycin (100%), and ciprofloxacin (62.5%). All the isolates were resistant to ampicillin and chloramphenicol. Multidrug resistances were found among most of the isolates.

Conclusion:

A high prevalence of enteric fever and drug resistance to most commonly prescribed antimicrobials were observed in this study. Those of old age with previous history of enteric infection were more affected by enteric fever. Health information should be given about the transmission, prevention of enteric fever, and antimicrobial use. The treatment of enteric fever should be supported by antimicrobial susceptibility tests in the study areas.

Characterization of a Salmonella Enteritidis bacteriophage showing broad lytic activity against Gram-negative enteric bacteria

In this study, we sought to isolate Salmonella Enteritidis-specific lytic bacteriophages (phages), and we found a lytic phage that could lyse not only S. Enteritidis but also other Gramnegative foodborne pathogens. This lytic phage, SS3e, could lyse almost all tested Salmonella enterica serovars as well as other enteric pathogenic bacteria including Escherichia coli, Shigella sonnei, Enterobacter cloacae, and Serratia marcescens. This SS3e phage has an icosahedral head and a long tail, indicating belong to the Siphoviridae. The genome was 40,793 base pairs, containing 58 theoretically determined open reading frames (ORFs). Among the 58 ORFs, ORF49, and ORF25 showed high sequence similarity with tail spike protein and lysozyme-like protein of Salmonella phage SE2, respectively, which are critical proteins recognizing and lysing host bacteria. Unlike SE2 phage whose host restricted to Salmonella enterica serovars Enteritidis and Gallinarum, SS3e showed broader host specificity against Gram-negative enteric bacteria; thus, it could be a promising candidate for the phage utilization against various Gram-negative bacterial infection including foodborne pathogens.

An Appraisal of the Clinical Features of Pediatric Enteric Fever: Systematic Review and Meta-analysis of the Age-Stratified Disease Occurrence

Children bear a substantial proportion of the enteric fever disease burden in endemic areas. Controversy persists regarding which age groups are most affected, leading to uncertainty about optimal intervention strategies. We performed a systematic review and meta-analysis of studies in Asia and Africa to compare the relative proportion of children with enteric fever in the age groups <5 years, 5–9 years, and 10–14 years. Overall, studies conducted in Africa showed a relatively smaller occurrence of disease in the youngest age group, whereas in Asia the picture was more mixed with a very large degree of heterogeneity in estimates. The clinical features of enteric fever reviewed here differ between younger and older children and adults, likely leading to further uncertainty over disease burden. It is evident from our review that preschool children and infants also contribute a significant proportion of disease burden but have not been adequately targeted via vaccination programs, which have been focusing primarily on school-based vaccination campaigns.

Draft Genome Sequence of a Salmonella enterica Serovar Typhi Strain Resistant to Fourth-Generation Cephalosporin and Fluoroquinolone Antibiotics

Typhoid is endemic in developing countries. We report here the first draft genome sequence of a Salmonella enterica serovar Typhi clinical isolate from Pakistan exhibiting resistance to cefepime (a fourth-generation cephalosporin) and fluoroquinolone antibiotics, two of the last-generation therapies against this pathogen. The genome is ~4.8 Mb, with two putative plasmids.

Mechanisms of resistance to quinolones in Salmonella Typhimurium from patients with infectious diarrhea

This study investigated the mechanisms of resistance of 36 quinolone-resistant Salmonella Typhimurium strains isolated from outpatients with infectious diarrhea in Beijing Tian Tan Hospital between 2013 and 2015. The resistance spectrum of the 36 strains was measured using a broth dilution method. Class 1 integrons harboring the β-lactamase gene and mutations in quinolone resistance determining regions were also investigated. All 36 quinolone-resistant Salmonella Typhimurium strains were found to be multidrug-resistant and the majority of these strains harbored Class 1 integrons. These findings study suggests that strategies for determining resistance spectrums should be implemented with greater urgency.

Antimicrobial Resistance of Salmonella enterica Serovars Typhi and Paratyphi Isolates from a General Hospital in Karawaci, Tangerang, Indonesia: A Five-Year Review

Typhoid and paratyphoid fever known as enteric fever pose important global public health problem, with 21.6 million cases and approximately 250,000 deaths annually. It is a prevalent disease in Indonesia, but data on the antimicrobial resistance pattern is limited. This study aim was to provide data on the antimicrobial resistance pattern of S. Typhi and S. Paratyphi bloodstream isolates in a general hospital in Karawaci, Tangerang, Banten, Indonesia, during the period of January 2011 to December 2015. Susceptibility against antimicrobials was detected according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Out of a total of 168 isolates 55.4% were S. Typhi and 44.6% S. Paratyphi A. Most of the isolates, 92.9%, were from children aged 6–18 years and adult population. There was low resistance of S. Typhi against ampicillin, trimethoprim-sulfamethoxazole, ceftriaxone, ciprofloxacin, and levofloxacin, similar to previous studies in Indonesia. In the 2011–2015 period, resistance rates against most antimicrobials and MDR rate of S. Typhi and S. Paratyphi were low, emphasizing that there is a distinct epidemiological dynamic of the enteric fever in Indonesia.

Antimicrobial resistance and molecular subtypes of Salmonella enterica serovar Typhi isolates from Kolkata, India over a 15 years period 1998-2012

Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), remains an unresolved public health problem in India. Emergence of antimicrobial resistant strains poses a great concern for typhoid treatment and influences reshaping of current S. Typhi population. We included representative S. Typhi strains (n=164) from retrospective studies, both community and hospital based, conducted at National Institute of Cholera and Enteric Diseases, Kolkata during 15 years period (1998-2012) to analyze their antimicrobial resistance (AMR) profiles, mechanism of AMR and molecular subtypes of the strains. More than 60% of the S. Typhi isolates were obtained from community based studies. During the study period, steady decline (46.4%-15.6%) in isolation of multidrug-resistant (MDR, resistant to ampicillin, chloramphenicol and co-trimoxazole) S. Typhi was noticed with parallel increase of nalidixic acid-resistant (NAL^R) strains (60.7%-93.8%) and ciprofloxacin resistant (CIP^R) strains (0%-25%). Of 53 MDR strains, 46 (86.8%) were NAL^R showing decreased ciprofloxacin susceptible (DCS) (MIC for ciprofloxacin 0.12-0.5μg/ml) phenotype. Conjugative IncHI1 (230kb) and non-conjugative non-IncHI1 (180kb) plasmids were found in 23 (43.4%) and 14 (26.4%) MDR strains respectively, plasmid was absent in 16 (30.2%) MDR strains. MDR strains with or without plasmid shared the same set of resistance genes (bla_TEM-1, catA1, sul1, sul2, strA and strB) and class 1 integron possessing dfrA7 gene cassette. Two S. Typhi strains harbored 50kb transferrable plasmids carrying dfrA15 and aadA1 gene cassettes in class 1 integron. The majority of the strains (135/164, 82.3%) belonged to H58 haplotype. Among the MDR isolates, fluoroquinolone resistant or combined resistant isolates (n=147), 127 (86.4%) were H58 and 20 (13.6%) belonged to non-H58. NAL^RS. Typhi strains with decreased susceptibility or resistance to ciprofloxacin had point mutation(s) in quinolone resistance-determining region of gyrA and parC genes. Pulsed-field gel electrophoresis showed more diversity among NAL^RS. Typhi than MDR strains. Results of this study generated information useful for better understanding of the disease epidemiology and its control in endemic settings.

Antibiogram of Salmonella Isolates: Time to Consider Antibiotic Salvage

INTRODUCTION

Enteric fever is a major problem especially in developing countries. Timely and appropriate treatment plays a very important role in reducing the mortality. Fluoroquinolones and cephalosporins are the treatment options for enteric fever. Recent studies have shown that it is time to reconsider the use of earlier antibiotics.

AIM

The study was aimed to know whether salvage is possible and to avoid treatment failures following fluoroquinolone usage.

MATERIALS AND METHODS

A one year retrospective data of Salmonella species isolated from 319 blood samples from our hospital and other diagnostic centers were studied. Demographic data, organism isolated and their changing pattern of antibiogram were analysed.

RESULTS

Out of 319 Salmonella isolates, 52.4% (167) was Salmonella typhi (S. typhi) and 47.6% (152) Salmonella paratyphi A (S. paratyphi A), with a male preponderance. Most of the salmonellae were isolated in the months of June and July, with the majority being in the 1-10 and 21-30 years age groups. Both species were highly susceptible to chloramphenicol (95.2% and 100%) followed by third generation cephalosporins (97% and 98%), cotrimoxazole (95.8% and 98.6%) and ampicillin (94.6% and 93.4%) respectively. Highest resistance was seen for nalidixic acid (90.4% and100%) among both S. typhi and S. paratyphi A isolates followed by ciprofloxacin (62.2% and 54.6%) respectively. MDR to first line drugs was observed in a small proportion of S. typhi (1.7%) only.

CONCLUSION

The frequency of isolation of S. typhi and S. paratyphi A are in equal proportion and enteric fever is more prevalent in younger age group. It is ideal to adopt bivalent vaccination in Universal immunization schedule. The isolates show sensitivity to first line drugs, paving the way for salvage of the earlier drugs. Cephalosporins still remain the treatment of choice in MDR salmonella isolates.

High prevalence of typhoidal Salmonella enterica serovars excreting food handlers in Karachi-Pakistan: a probable factor for regional typhoid endemicity

BACKGROUND

Typhoid fever is the persistent cause of morbidity worldwide. Salmonella enterica serovar's carriers among food handlers have the potential to disseminate this infection on large scale in the community. The purpose of this study was to determine the prevalence of typhoidal S. enterica serovars among food handlers of Karachi.

METHODS

This cross-sectional study was conducted in Karachi metropolis. A total of 220 food handlers were recruited on the basis of inclusion criteria from famous food streets of randomly selected five towns of Karachi. Three consecutive stool samples were collected from each food handler in Carry Blair transport media. Culture, biochemical identification, serotyping, and antimicrobial susceptibility tests for S. enterica serovars were done.

RESULTS

Out of 220 food handlers, 209 consented to participate, and among them, 19 (9.1%) were positive for S. enterica serovars. Serotyping of these isolates showed that 9 (4.3%) were typhoidal S. serovars while 10 (4.7%) were non-typhoidal S. serovars. Of the typhoidal S. serovars, 7 were S. enterica serovar Typhi and 1 each of S. enterica serovar Paratyphi A and B. The resistance pattern of these isolates showed that 77.7% were resistant to ampicillin and 11.1% to cotrimoxazole. All typhoidal S. enterica serovar isolates were sensitive to chloramphenicol, ceftriaxone, cefixime, nalidixic acid, and ofloxacin.

CONCLUSIONS

Carrier rate of typhoidal S. enterica serovars in food handlers working in different food streets of Karachi is very high. These food handlers might be contributing to the high endemicity of typhoid fever in Karachi, Pakistan.

Epidemiology, Clinical Presentation, Laboratory Diagnosis, Antimicrobial Resistance, and Antimicrobial Management of Invasive Salmonella Infections

Salmonella enterica infections are common causes of bloodstream infection in low-resource areas, where they may be difficult to distinguish from other febrile illnesses and may be associated with a high case fatality ratio. Microbiologic culture of blood or bone marrow remains the mainstay of laboratory diagnosis. Antimicrobial resistance has emerged in Salmonella enterica, initially to the traditional first-line drugs chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole. Decreased fluoroquinolone susceptibility and then fluoroquinolone resistance have developed in association with chromosomal mutations in the quinolone resistance-determining region of genes encoding DNA gyrase and topoisomerase IV and also by plasmid-mediated resistance mechanisms. Resistance to extended-spectrum cephalosporins has occurred more often in nontyphoidal than in typhoidal Salmonella strains. Azithromycin is effective for the management of uncomplicated typhoid fever and may serve as an alternative oral drug in areas where fluoroquinolone resistance is common. In 2013, CLSI lowered the ciprofloxacin susceptibility breakpoints to account for accumulating clinical, microbiologic, and pharmacokinetic-pharmacodynamic data suggesting that revision was needed for contemporary invasive Salmonella infections. Newly established CLSI guidelines for azithromycin and Salmonella enterica serovar Typhi were published in CLSI document M100 in 2015.

Abdominal lymphadenopathy: an atypical presentation of enteric fever

This is a case report of a patient who presented to the Aga Khan University Hospital with generalized abdominal lymphadenopathy and high-grade fever. Due to ambiguous clinical findings, which were suggestive of either abdominal tuberculosis, or a lymphoma, the patient was started on empirical anti-tuberculous treatment due to the endemicity of tuberculosis in this region. The blood culture reports, however, were reported to grow colonies of Salmonella paratyphi A; thus the diagnosis of the patient was changed to enteric fever, and the patient improved on the subsequently started therapy of ceftriaxone 2,000 mg bid. To the best of our knowledge, this is the first reported case of a patient suffering from enteric fever whose primary clinical findings were abdominal lymphadenopathy and fever.

Systematic Review of Antibiotic Resistance Rates Among Gram-Negative Bacteria in Children With Sepsis in Resource-Limited Countries

BACKGROUND

Gram-negative antimicrobial resistance (AMR) is of global concern, yet there are few reports from low- and low-middle-income countries, where antimicrobial choices are often limited.

METHODS

This study offers a systematic review of PubMed, Embase, and World Health Organization (WHO) regional databases of Gram-negative bacteremia in children in low- and low-middle-income countries reporting AMR since 2001.

RESULTS

Data included 30 studies comprising 71 326 children, of whom 7056 had positive blood cultures, and Gram-negative organisms were isolated in 4710 (66.8%). In neonates, Klebsiella pneumoniae median resistance to ampicillin was 94% and cephalosporins 84% in Asia; 100% and 50% in Africa. Large regional variations in resistance rates to commonly prescribed antibiotics for Salmonella spp. were identified. Multidrug resistance (resistance to ampicillin, chloramphenicol, and cotrimoxazole) was present in 30% (interquartile range [IQR], 0-59.6) in Asia and 75% (IQR, 30-85.4) in Africa.

CONCLUSIONS

There is a need for an international pediatric antimicrobial resistance surveillance system that collects local epidemiological data to improve the evidence base for the WHO guidance for childhood Gram-negative bacteremia.

Salmonella blood stream infections in a tertiary care setting in Ghana

Background

Despite the clinical significance of Salmonella infections, surveillance data worldwide remains limited and is more so exemplified by the lack of reports from Africa especially in eastern, central and western Africa. This study reports on Salmonella serotypes as significant causes of blood stream infections (BSI) and multidrug antibiotic resistance at Korle-Bu Teaching Hospital in Accra, Ghana.

Methods

Antibiogram patterns, seasonal variations in disease incidence and predisposing factors for infection with Salmonella serotypes were analyzed retrospectively over a 4-year period from January 2010 to December 2013. Blood cultures were processed with BACTEC 9240 blood culture system. Speciation was done with BBL Crystal Enteric/Nonfermenter identification system®, and with slide agglutination using specific antisera. Antimicrobial susceptibility testing was carried out by the Kirby-Bauer disc diffusion method according to Clinical and Laboratory Standard Institute guidelines.

Results

We report a 6.5% (n = 181/2768) prevalence of Salmonella bacteraemia at the Korle-Bu Teaching Hospital; with a preponderance of non-typhoidal salmonellae (NTS) over typhoidal salmonella (TS) (n = 115/181, 63.5% versus n = 66/181, 36.5%; P-value <0.002). Children under 5 years bore the brunt of the disease (n = 93/174, 53.4%). Resistance to ciprofloxacin (n = 1/127, 0.7%), amikacin (n = 3/81, 3.7%), and cefotaxime (n = 6/99, 6.1%) remained low, despite high levels of multidrug resistant Salmonella phenotypes (n = 81/181, 44.2%). In multivariate analysis, and among patients with Salmonella BSI, those < 1 year old had reduced risk of non-typhoidal infections [Odds ratio, 0.51; 95% confidence interval (95% CI), 0.16-0.92, P-value 0.021]. Similarly, patients with cefuroxime resistant strans were at increased risk of having multidrug resistant Salmonella BSI (OR, 8.97; 95% CI, 3.62-24.15; P-value, 0.001).

Conclusions

Salmonellae, predominantly NTS, account for a reasonable low proportion of positive blood cultures in our tertiary care setting; but with significant multidrug resistant phenotypes and low ciprofloxacin and cefotaxime resistance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-014-0697-7) contains supplementary material, which is available to authorized users.

Bloodstream infections at a tertiary referral hospital in Yangon, Myanmar

BACKGROUND

Data regarding characteristics of bloodstream infections in Myanmar are limited.

METHODS

Blood culture results from all outpatients and inpatients were extracted from records of the Clinical Microbiology Laboratory, Yangon General Hospital, for the period 2005 through 2013.

RESULTS

Of 3865 blood cultures performed, 449 (11.6%) were positive for a pathogenic organism. Gram-negative bacteria was the most common organism group, accounting for 246 (55.5%) of 449 isolations. Staphylococcus aureus was the most common isolate, detected in 171 (38.1%) of 449 blood cultures. From 2005-2008 to 2009-2013 the proportion of all pathogenic isolates that were Gram-positive declined from 52.8% (167/316) to 20.3% (27/133) (p<0.001), whereas the proportion of Gram-negative bacteria rose from 45.6% (144/316) to 78.9% (105/133) (p<0.001), with non-fermentative bacilli accounting for much of this increase. Antimicrobial susceptibility testing demonstrated a high prevalence resistance of S. aureus to first-line antimicrobials such as erythromycin, penicillin and oxacillin. More than half of tested Escherichia coli and Citrobacter species showed resistance to amoxicillin-clavulanic acid, ceftriaxone or gentamicin.

CONCLUSIONS

Bloodstream infections are common among patients receiving blood culture at a tertiary hospital in Yangon, Myanmar. Our findings suggest that antimicrobial resistance among invasive bacteria is common, similar to patterns described elsewhere in the region, and highlight the need for locally adapted antimicrobial guidelines for sepsis management.

Antimicrobial resistance, virulence profiles and molecular subtypes of Salmonella enterica serovars Typhi and Paratyphi A blood isolates from Kolkata, India during 2009-2013

Enteric fever, caused by Salmonella enterica, remains an unresolved public health problem in India and antimicrobial therapy is the main mode of treatment. The objective of this study was to characterize the Salmonella enterica isolates from Kolkata with respect to their antimicrobial resistance (AMR), virulence profiles and molecular subtypes. Salmonella enterica blood isolates were collected from clinically suspected enteric fever patients attending various hospitals in Kolkata, India from January 2009 to June 2013 and were tested for AMR profiles by standard protocols; for resistance gene transfer by conjugation; for resistance and virulence genes profiles by PCR; and for molecular subtypes by Pulsed Field Gel Electrophoresis (PFGE). A total of 77 Salmonella enterica serovar Typhi (S. Typhi) and 25 Salmonella enterica serovar Paratyphi A (S. Paratyphi A) from Kolkata were included in this study. Although multidrug resistance (resistance to chloramphenicol, ampicillin, co-trimoxazole) was decreasing in S. Typhi (18.2%) and absent in S. Paratyphi A, increased resistance to fluoroquinolone, the current drug of choice, caused growing concern for typhoid treatment. A single, non-conjugative non-IncHI1 plasmid of 180 kb was found in 71.4% multidrug resistant (MDR) S. Typhi; the remaining 28.6% isolates were without plasmid. Various AMR markers (blaTEM-1, catA, sul1, sul2, dfrA15, strA-strB) and class 1 integron with dfrA7 gene were detected in MDR S. Typhi by PCR and sequencing. Most of the study isolates were likely to be virulent due to the presence of virulence markers. Major diversity was not noticed among S. Typhi and S. Paratyphi A from Kolkata by PFGE. The observed association between AMR profiles and S. Typhi pulsotypes might be useful in controlling the spread of the organism by appropriate intervention. The study reiterated the importance of continuous monitoring of AMR and molecular subtypes of Salmonella isolates from endemic regions for better understanding of the disease epidemiology.

Estimating the burden of paratyphoid a in Asia and Africa

Despite the increasing availability of typhoid vaccine in many regions, global estimates of mortality attributable to enteric fever appear stable. While both Salmonella enterica serovar Typhi (S. Typhi) and serovar Paratyphi (S. Paratyphi) cause enteric fever, limited data exist estimating the burden of S. Paratyphi, particularly in Asia and Africa.

We performed a systematic review of both English and Chinese-language databases to estimate the regional burden of paratyphoid within Africa and Asia. Distinct from previous reviews of the topic, we have presented two separate measures of burden; both incidence and proportion of enteric fever attributable to paratyphoid. Included articles reported laboratory-confirmed Salmonella serovar classification, provided clear methods on sampling strategy, defined the age range of participants, and specified the time period of the study.

A total of 64 full-text articles satisfied inclusion criteria and were included in the qualitative synthesis. Paratyphoid A was commonly identified as a cause of enteric fever throughout Asia. The highest incidence estimates in Asia came from China; four studies estimated incidence rates of over 150 cases/100,000 person-years. Paratyphoid A burden estimates from Africa were extremely limited and with the exception of Nigeria, few population or hospital-based studies from Africa reported significant Paratyphoid A burden.

While significant gaps exist in the existing population-level estimates of paratyphoid burden in Asia and Africa, available data suggest that paratyphoid A is a significant cause of enteric fever in Asia. The high variability in documented incidence and proportion estimates of paratyphoid suggest considerable geospatial variability in the burden of paratyphoid fever. Additional efforts to monitor enteric fever at the population level will be necessary in order to accurately quantify the public health threat posed by S. Paratyphi A, and to improve the prevention and treatment of enteric fever.

Enteric fever due to Salmonella enterica serovar Typhi (S. Typhi) and serovar Paratyphi (S. Paratyphi A, B, C) remains a global public health concern. While numerous studies have estimated the levels or burden of S. Typhi, there are only limited data estimating the burden of S. Paratyphi A, particularly in Asia and Africa. We reviewed both English and Chinese-language databases for estimates of the regional burden within Africa and Asia, including new paratyphoid A cases/year and proportion of enteric fever cases attributable to paratyphoid A. S. Paratyphi A appears to constitute a significant proportion of all cases of enteric fever in Asia, though population level estimates are limited, especially in Africa. There was high variability in reported paratyphoid A burden estimates, which suggests considerable geospatial variability in the burden of paratyphoid fever. Improved efforts to monitor enteric fever at the population level are warranted in order to correctly measure the public health threat posed by S. Paratyphi A and to determine the potential need for S. Paratyphi specific prevention and treatment interventions.

Antimicrobial resistance in Salmonella enterica serovar typhi and paratyphi in South Asia-current status, issues and prospects

The human race owes a debt of gratitude to antimicrobial agents, penicillin and its successors that have saved people from tremendous pain and suffering in the last several decades. Unfortunately, this consideration is no more true, as millions of people are prone to the challenging threat of emergence of antimicrobial resistance worldwide and the menace is more distressing in developing countries. Comparable with other bacterial species, Salmonella enterica serovar Typhi (S. typhi) and Paratyphi (S. paratyphi) have been evolving multidrug resistance (MDR) against a wide array of antibiotics, including chloramphenicol, ampicillin and co-trimoxazole, and globally affecting 21 million people with 220,000 deaths each year. S. typhi and S. paratyphi infections are also endemic in South Asia and a series of antibiotics used to treat these infections, have been losing efficacy against enteric fever. Currently, quinolones are regarded as a choice to treat MDR Salmonella in these regions. Travel-related cases of enteric fever, especially from South Asian countries are the harbinger of the magnitude of MDR Salmonella in that region. Conclusively, the MDR will continue to grow and the available antimicrobial agents would become obsolete. Therefore, a radical and aggressive approach in terms of rational use of antibiotics during treating infections is essentially needed.

Antibiotic resistance-the need for global solutions

The causes of antibiotic resistance are complex and include human behaviour at many levels of society; the consequences affect everybody in the world. Similarities with climate change are evident. Many efforts have been made to describe the many different facets of antibiotic resistance and the interventions needed to meet the challenge. However, coordinated action is largely absent, especially at the political level, both nationally and internationally. Antibiotics paved the way for unprecedented medical and societal developments, and are today indispensible in all health systems. Achievements in modern medicine, such as major surgery, organ transplantation, treatment of preterm babies, and cancer chemotherapy, which we today take for granted, would not be possible without access to effective treatment for bacterial infections. Within just a few years, we might be faced with dire setbacks, medically, socially, and economically, unless real and unprecedented global coordinated actions are immediately taken. Here, we describe the global situation of antibiotic resistance, its major causes and consequences, and identify key areas in which action is urgently needed.

Typhoid Fever in an inner city hospital: a 5-year retrospective review

BACKGROUND

Typhoid is a leading cause of fever in returning travelers. The prevalence is highest in migrants visiting friends and relatives (VFR travelers) in the Indian subcontinent, where reports of resistance have been of concern. This study is a retrospective analysis of patients with typhoid, seen over a 5-year period, in a tertiary center that serves a large immigrant population.

METHODS

Patients with blood cultures positive for Salmonella Typhi were identified between 2006 and 2010. Charts were reviewed for demographic data, travel history, symptoms and signs, basic laboratory results, susceptibility profiles, treatment, and clinical course. Resistance to nalidixic acid was used as a marker of decreased susceptibility to quinolones.

RESULTS

Seventeen patients were identified with S Typhi. The median age was 12 years (range: 2-47 y) and 94% (16 of 17) were hospitalized with a median stay of 7 days; two were admitted to the intensive care unit. Fourteen patients (82%) had a history of recent travel. Twelve were VFR travelers in Bangladesh and Pakistan and two had recently immigrated. In our study, typhoid patients had low eosinophil counts and elevated transaminases. Seventy-six percent (12 of 17) of all isolates were resistant to nalidixic acid, 23.5% (4 of 17) were resistant to ampicillin and co-trimoxazole, and one was resistant to ciprofloxacin. All isolates were susceptible to third-generation cephalosporins.

CONCLUSIONS

Younger VFR travelers appear to be at greater risk of acquiring infection and developing complications. Absolute eosinopenia and increased liver function test values could be useful early diagnostic clues in a returning traveler with fever, once malaria has been excluded. There was a high rate of decreased susceptibility to fluoroquinolones, confirming that the use of third-generation cephalosporins or macrolides in patients from the Indian subcontinent is most appropriate. Prevention in VFR travelers to South Asia is critical and efforts should be targeted at better education and pre-travel immunization.

Salmonella infections: an update on epidemiology, management, and prevention

Salmonella species are a group of Gram-negative enterobacteria and known human pathogens in developing as well as industrialized countries. Despite significant advances in sanitation, provision of potable water, and highly controlled food chain surveillance, transmission of Salmonella spp. continues to affect communities, preferentially children, worldwide. This review summarizes updated concepts on typhoidal and non-typhoidal Salmonella infections, starting with a historical perspective that implicates typhoid Salmonella as a significant human pathogen since ancient times. We describe the epidemiology of this pathogen with emphasis on the most recent non-typhoidal Salmonella outbreaks in industrialized countries and continued outbreaks of typhoid Salmonella in underserved countries. An overview of clinical aspects of typhoid and non-typhoid infections in developing and industrialized countries, respectively, is provided, followed by a description on current treatment concepts and challenges treating multidrug-resistant Salmonella infections. We conclude with prevention recommendations, and recent research studies on vaccine prevention.

One health national programme across species on zoonoses: a call to the developing world

Zoonoses constitute 868 (61%) of all known infectious diseases, 75% of the infections considered ‘emerging’ are zoonoses. Developed nations have national programmes, adjoining “One Health” concept to combat zoonoses, whereas inadequacies exist in developing nations. As a case study, role of national programmes in India, a developing nation with a large human and animal population, was explored, as we did have acquaintance of it. Data from PubMed was extracted using keywords “Zoonoses AND Prevalence/Incidence AND India AND Human OR Animal” till 2009. Additionally, some individual disease keywords were used for extraction, which were missed by the above comprehensive search terms. On appraisal, the health sector in India has only a few national programme on zoonoses where as none exists in animal husbandry sector. In the struggle against zoonoses -a major constituent of emerging infections, a system approach based, one national programme is urgently required for the developing world.

Antimicrobial susceptibility of bacterial isolates from community acquired infections in Sub-Saharan Africa and Asian low and middle income countries

OBJECTIVE

Antimicrobial resistance has arisen across the globe in both nosocomial and community settings as a consequence of widespread antibiotic consumption. Poor availability of laboratory diagnosis means that resistance frequently goes unrecognised and may only be detected as clinical treatment failure. In this review, we provide an overview of the reported susceptibility of common community acquired bacterial pathogens in Sub-Saharan Africa and Asia to the antibiotics that are most widely used in these areas.

METHODS

We reviewed the literature for reports of the susceptibility of prevalent pathogens in the community in SSA and Asia to a range of commonly prescribed antibiotics. Inclusion criteria required that isolates were collected since 2004 and that they were obtained from either normally sterile sites or urine. The data were aggregated by region and by age group.

RESULTS

Eighty-three studies were identified since 2004 which reported the antimicrobial susceptibilities of common bacterial pathogens. Different methods were used to assess in-vitro susceptibility in the different studies. The quality of testing (evidenced by resistance profiles) also varied considerably. For Streptococcus pneumoniae and Neisseria meningitidis most drugs maintained relatively high efficacy, apart from co-trimoxazole to which there were high levels of resistance in most of the pathogens surveyed.

CONCLUSIONS

Compared with the enormous infectious disease burden and widespread use of antibiotics there are relatively few reliable data on antimicrobial susceptibility from tropical Asia and Africa upon which to draw firm conclusions, although it is evident that many commonly used antibiotics face considerable resistance in prevalent bacterial pathogens. This is likely to exacerbate morbidity and mortality. Investment in improved antimicrobial susceptibility testing and surveillance systems is likely to be a highly cost-effective strategy and should be complemented by centralized and readily accessible information resources.

High burden of antimicrobial resistance in Asia

Antimicrobial resistance is associated with high mortality rates and high medical costs. Marked variations in the resistance profiles of bacterial and fungal pathogens as well as the quality of public hygiene have had a considerable impact on the effectiveness of antimicrobial agents in Asian countries. In Asia, one of the epicentres of antimicrobial drug resistance, there is an alarming number of antibiotic-resistant species, including penicillin- and erythromycin-resistant Streptococcus pneumoniae, ampicillin-resistant Haemophilus influenzae, multidrug-resistant (MDR) Acinetobacter baumannii, extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae (particularly mediated by CTX-M-9, CTX-M-14 and CTX-M-15), New Delhi metallo-β-lactamase 1 (NDM-1)-producing Enterobacteriaceae, MDR Salmonella enterica serotypes Choleraesuis and Typhi, carbapenem-resistant A. baumannii (OXA-58 and OXA-23 carbapenemases) and azole-resistant Candida glabrata. A few clones of MDR A. baumannii and hospital-acquired meticillin-resistant Staphylococcus aureus (MRSA) have been widely disseminated in hospital settings in Asia, and K. pneumoniae carbapenemase (KPC)-producing K. pneumoniae strains have been widely distributed in China. In addition, the emergence of extensively drug-resistant Mycobacterium tuberculosis (XDR-TB) has illustrated the need for regular monitoring of resistance profiles of clinical isolates as well as the deliberative use of fluoroquinolones. Continuous surveillance of resistance data from clinical isolates as well as implementation of strict infection control policies in healthcare settings are required to mitigate the progression of antimicrobial resistance.

Analysis of Salmonella enterica serotype paratyphi A gene expression in the blood of bacteremic patients in Bangladesh

BACKGROUND

Salmonella enterica serotype Paratyphi A is a human-restricted cause of paratyphoid fever, accounting for up to a fifth of all cases of enteric fever in Asia.

METHODOLOGY/PRINCIPAL FINDINGS

In this work, we applied an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS), and cDNA hybridization-microarray technology to identify S. Paratyphi A transcripts expressed by bacteria in the blood of three patients in Bangladesh. In total, we detected 1,798 S. Paratyphi A mRNAs expressed in the blood of infected humans (43.9% of the ORFeome). Of these, we identified 868 in at least two patients, and 315 in all three patients. S. Paratyphi A transcripts identified in at least two patients encode proteins involved in energy metabolism, nutrient and iron acquisition, vitamin biosynthesis, stress responses, oxidative stress resistance, and pathogenesis. A number of detected transcripts are expressed from PhoP and SlyA-regulated genes associated with intra-macrophage survival, genes contained within Salmonella Pathogenicity Islands (SPIs) 1-4, 6, 10, 13, and 16, as well as RpoS-regulated genes. The largest category of identified transcripts is that of encoding proteins with unknown function. When comparing levels of bacterial mRNA using in vivo samples collected from infected patients to samples from in vitro grown organisms, we found significant differences for 347, 391, and 456 S. Paratyphi A transcripts in each of three individual patients (approximately 9.7% of the ORFeome). Of these, expression of 194 transcripts (4.7% of ORFs) was concordant in two or more patients, and 41 in all patients. Genes encoding these transcripts are contained within SPI-1, 3, 6 and 10, PhoP-regulated genes, involved in energy metabolism, nutrient acquisition, drug resistance, or uncharacterized genes. Using quantitative RT-PCR, we confirmed increased gene expression in vivo for a subset of these genes.

CONCLUSION/SIGNIFICANCE

To our knowledge, we describe the first microarray-based transcriptional analysis of a pathogen in the blood of naturally infected humans.

The expanding spectrum of disease due to salmonella: an international perspective

Human disease due to Salmonella infections appears to be on the rise worldwide. Despite the availability of vaccines and generally effective antibiotic therapy, salmonellosis, in the forms of gastroenteritis and enteric fever, remains a major cause of morbidity and mortality in many developing countries, especially in young children and immunocompromised hosts. In certain highly endemic areas of South and Southeast Asia, the emergence of quinolone-resistant and multidrug-resistant strains of Salmonella contribute to the magnitude of the problem. In the United States and Europe, a low but consistent rate of disease appears to be primarily related to ingestion of contaminated poultry, lapses in sanitary agricultural practices, and importation of tainted vegetable products. An improved understanding of the molecular basis of bacterial resistance and improved design and expanded use of vaccines provide hope for containing the spread and reducing morbidity of the international spectrum of disease due to Salmonella pathogens.

Characterization of antimicrobial resistance, molecular and phage types ofSalmonella entericaserovar Typhi isolations

Isolation rates in Canada ofSalmonella entericaserovar Typhi increased from 0·29 to 0·55 isolations/100 000 population during 2000–2006. Although no ciprofloxacin resistance was detected, nalidixic acid resistance increased from 41% to 80%. Multidrug-resistantS. Typhi represented 18% of the strains tested. Pulsed-field gel electrophoresis (PFGE) analysis of 222 isolates resulted in 91 distinct patterns clustering into four major genetic similarity groups. The five most frequently occurring PFGE patterns accounted for 46% of the isolates. Drug-resistant isolates predominantly occurred in one PFGE similarity group. There were 39 phage types identified in 826 isolates analysed with 60% described by five phage types; 134 were untypable. The phage types associated with multidrug resistance were phage types 53, B1, D1, E1, E9, G3 and M1. Improved integration of epidemiological and laboratory case data will facilitate the protection of public health in Canada during an era of increasing travel and globalization.

Elucidation of Antimicrobial Susceptibility Profiles and Genotyping of Salmonella enterica Isolates from Clinical Cases of Salmonellosis in New Mexico in 2008

In this study, we investigated the antimicrobial susceptibility profiles and the distribution of some well known genetic determinants of virulence in clinical isolates of Salmonella enterica from New Mexico. The minimum inhibitory concentrations (MICs) for various antimicrobials were determined by using the E-test strip method according to CLSI guidelines. Virulence genotyping was performed by polymerase chain reaction (PCR) using primers specific for known virulence genes of Salmonella enterica. Of 15 isolates belonging to 11 different serovars analyzed, one isolate of Salmonella Typhimurium was resistant to multiple drugs namely ampicillin, amoxicillin / clavulanic acid, chloramphenicol and tetracycline, that also harbored class 1 intergron, bla(TEM) encoding genes for β-lactamase, chloramphenicol acetyl transferase (cat1), plus floR, tet(C) and tet(G). This strain was phage typed as DT104. PCR analysis revealed the presence of invA, hilA, stn, agfA and spvR virulence genes in all the isolates tested. The plasmid-borne pefA gene was absent in 11 isolates, while 5 isolates lacked sopE. One isolate belonging to serogroup E4 (Salmonella Sombre) was devoid of multiple virulence genes pefA, iroB, shdA and sopE. These results demonstrate that clinical Salmonella serotypes from New Mexico used here are predominantly sensitive to multiple antimicrobial agents, but vary in their virulence genotypes. Information on antimicrobial sensitivity and virulence genotypes will help in understanding the evolution and spread of epidemic strains of Salmonella enterica in the region of study.

Simple Liver Cyst as a Focus of Salmonella paratyphi Abscess: A Case Report

Salmonellosis, endemic in various part of the world, is considered a differential diagnosis in a tropical traveller. Although it usually presents as gastroenteritis, its various clinical syndromes may vary from mild gastroenteritis to severe septicaemia including abscess formation, the later two being the most common cause of morbidity and mortality. Here we present a patient who returned to the UK after an overseas trip and was diagnosed with a pyogenic liver abscess with Salmonella paratyphi at a site of a pre-existing simple liver cyst.