Clinical Perspectives of Multiple and Extensively Drug-Resistant Typhoid; result from a tertiary care hospital from Pakistan.

INTRODUCTION: Typhoid fever remains a problem in developing countries, including Pakistan. The emergence of multidrug-resistant and, since 2016, of extensively drug-resistant cases is a continuous challenge for health care workers. The COVID-19 pandemic is making management more difficult. METHODOLOGY: In the present study, a total of 52 confirmed cases of typhoid have been studied during 2019. Detailed clinical features, complications and, lab findings were studied. Typhoid culture and sensitivity were recorded and patients were treated accordingly. Patients were asked about risk factors to aim at informing prevention. RESULTS: Out of the 52 having blood culture positive for Salmonella Typhi 47 (90.4%) and Salmonella Paratyphi 5 (9.6%), 4 (7.7%) were sensitive to first-line (Non-resistant), 11 (21.2%) MDR and 37 (71.2%) patient were XDR. One case was resistant to azithromycin. Nausea, vomiting or, abdominal pain was present in 12 (23%), abdominal distension present in 9 (17.3%), abdominal tenderness in 8 (15.4%), hepatomegaly in 10 (19.2%) and, splenomegaly in 22 (42.3%).There were ultrasound abnormalities in 58% of patients and GI complications in 19% of patients. No significant difference was found in clinical findings and complications between resistant and non-resistant cases. Only 23-27% of patients were aware of typhoid prevention and vaccination measures. CONCLUSIONS: The increasing prevalence of resistance and higher degree of complications seen in typhoid fever raises the concern further about prevention and effective infection management in the community as well as clinical settings. Moreover, judicial use of antibiotics is much needed in developing countries like Pakistan.

Salmonella Typhi and Salmonella Paratyphi prevalence, antimicrobial susceptibility profile and factors associated with enteric fever infection in Bahir Dar, Ethiopia.

Enteric fever (EF) is caused by Salmonella enterica serovars Typhi (S. Typhi) and Paratyphi (S. Paratyphi) causing significant health problems in developing countries including Ethiopia. Thus present study aimed to determine prevalence and antimicrobial resistance profile of S. Typhi and S. Paratyphi among EF suspected patients at Felege-Hiwot comprehensive specialized hospital, Bahir Dar, Ethiopia. Hospital based cross-sectional study was conducted from March-to-May 2020. Totally, 150 patients were included conveniently. Data were collected using questionnaires by face-to-face interview. Concurrently, venous blood and stool specimens were collected and processed following standard bacteriological technique. Antimicrobial susceptibility test (AST) was performed by disc diffusion method. Logistic regression was performed to identify factors associated with EF infection. The study indicated 5.3% EF prevalence where S. Typhi accounted 75%. S. Typhi and S. Paratyphi isolates were 100% sensitive to cephalosporins but at least 83.3% showed resistance against chloramphenicol and tetracycline. At least 66.7% of isolates were multidrug resistance (MDR). Using well water for drinking (AOR = 6.22, CI 1.4-27.5) and previous EF history (AOR = 10.74, CI 2.01-55.9) were significantly associated with EF infection. Thus high bacterial prevalence and MDR isolates was observed. Therefore, health professionals should consider AST and use antibiotics with cautions for EF patient management.

Changes in antimicrobial resistance and molecular attributes of Salmonellae causing enteric fever in Kolkata, India, 2014-2018.

Globally, enteric fever caused by Salmonella Typhi (S. Typhi, ST) and S. Paratyphi A (SPA) remain one of the major diseases of public health importance. In this study, a total of 457 (380 ST, 77 SPA) blood isolates were collected from three tertiary care hospitals in Kolkata during 2014-18. Additionally, 66 (3.4%) ST and 5 (0.25%) SPA were recovered from blood culture of 1962 patients attending OPD of one pediatric hospital during 2016-18. The study isolates were tested for antimicrobial resistance (AMR) profiles; AMR genes; molecular sub-types by PFGE, MLVA and CRISPR. Among the total 446 ST and 82 SPA isolates, fluoroquinolone (FQ) resistance was very common in both serovars. Ciprofloxacin resistance of 24.9% and 9.8% & ofloxacin resistance of 20.9% and 87.8% were found in ST and SPA respectively. Majority (>70%) of the isolates showed decreased susceptibility to ciprofloxacin (DCS). A single point mutation in gyrA gene (S83F) was responsible for causing DCS in 37.5% (n = 42/112) ST and 63% (n = 46/73) SPA isolates. Multidrug resistance (MDR) was found only in 3.4% ST isolates and encoded the genes blaTEM-1, catA, sul, strA-strB, class 1 integron with dfrA7. All MDR ST (n = 15) possessed non-conjugative non-IncHI1 (180 kb) plasmid except one having conjugative IncHI1 (230 kb) plasmid and one without plasmid. The MDR genes were integrated near chromosomal cyaA gene site in ST with/without the presence of plasmid (nonIncH1). Almost 65.7% resistant ST belonged to H58 haplotype. PFGE showed clonally related isolates with 81% similarity in ST and 87% in SPA. Similarly, CRISPR typing showed less diversity among the isolates. However, the isolates (ST and SPA) were found to be more diverse by MLVA typing (D value 0.987 and 0.938). The study reports decrease in MDR and increase in FQ resistance among typhoidal Salmonella isolates over the years giving interesting information for enteric fever treatment.

Discovery of seven novel mutations of gyrB, parC and parE in Salmonella Typhi and Paratyphi strains from Jiangsu Province of China.

OBJECTIVE: To investigate the prevalence of Salmonella Typhi and Paratyphi resistance to quinolones and characterize the underlying mechanism in Jiangsu Province of China. METHODS: Antimicrobial susceptibility testing was performed using Kirby-Bauer disc diffusion system. Quinolone resistance-determining region (QRDR), plasmid-mediated quinolone resistance (PMQR) determinant genes were detected by PCR and sequencing. RESULTS: Out of 239 Salmonella isolates, 164 were S. Typhi and 75 were S. Paratyphi. 128 (53.6%) Salmonella isolates were resistant to nalidixic acid; 11 (4.6%) isolates to ciprofloxacin and 66 (27.6%) isolates were intermediate to ciprofloxacin. QRDR were present in 69 S. Typhi isolates, among which mutation at codon 83 (n = 45) and 133 (n = 61) predominated. In S. Paratyphi, the most common mutations were detected in gyrA at codon 83(n = 24) and parC: T57S (n = 8). Seven mutations were first reported in Salmonella isolates including gyrB: S426G, parC: D79G and parE: [S498T, E543K, V560G, I444S, Y434S]. PMQR genes including qnrD1, qnrA1, qnrB4, aac (6')-Ib-cr4 and qnrS1 were detected in 1, 2, 3, 7 and 9 isolates, relatively. CONCLUSIONS: High resistance to quinolones in Salmonella remains a serious problem in Jiangsu, China. The presence of the novel mutations increases the complexity of quinolone-resistant genotypes and poses a threat to public health. Subject terms: Salmonella Typhi, Salmonella Paratyphi, antimicrobial resistance, QRDR, PMQR.

Isolation and Characterization of a Lytic Salmonella paratyphi Phage and Its Antibiofilm Activity Individually or Collaborative with Kanamycin Sulfate.

Salmonella is among the most serious of foodborne pathogens worldwide and distributed widely in the natural environment; in addition, it has caused severe medical problems and foodborne diseases. Bacterial biofilm was the multicellular community of microorganisms that attached to nonbiological and biological surfaces. Phages and their derivatives are ideal candidates for replacing and compensating antibiotic resistance problems in the future. In this study, a virulent phage of KM15 was isolated from pig slaughterhouse sump samples in Kunming, China. It belonged to the Siphoviridae family, and optimal growth temperature was 42°C, the pH of optimal preservation buffer was 6-7, optimal multiplicity of infection was 0.0001, and the genome size was 41,869 bp. The Salmonella paratyphi A and Salmonella paratyphi B have a broad spectrum of antibiotic resistance and were isolated from clinical patients in the First People's Hospital of Yunnan Province; fortunately, most of them can be lysed by phage KM15. Collaboration of phage KM15 and kanamycin sulfate has a better antibiofilm effect than KM15 and kanamycin sulfate alone, in low-concentration bacterial culture; KM15 has better antibiofilm effect than kanamycin sulfate in high-concentration bacterial culture. The data of this study provided a strong evidence of application of phage to reduce the growth of Salmonella biofilm, which was important for public health.

[Typhoid and paratyphoid fever]. / Typhus abdominalis und Paratyphus.

Typhoid fever and paratyphoid fever are systemic infectious diseases of global significance caused by Salmonella enterica subspecies enterica Serovar Typhi (short name: Salmonella Typhi) or Serovar Paratyphi (short name: Salmonella Paratyphi). The course of these fecal-orally transmitted diseases is mainly characterized by a high fever. Left untreated, the course of typhoid fever can be severe and lethal. The infection is almost always acquired outside of Europe (mainly in India) and is notifiable in Germany, Austria and Switzerland. Paratyphoid is an attenuated disease of typhoid fever caused by Salmonella Paratyphi. Available vaccines only protect against Salmonella Typhi. Antibiotic resistance reflects the situation in endemic countries and shows a worrying increase of multi-drug resistant isolates. Currently, third-generation cephalosporins such as ceftriaxone are recommended as first-line therapy; if sensitive to quinolones, fluoroquinolones such as ciprofloxacin may continue to be administered. Crucial preventive measures for travelers to endemic regions include consistent water and food hygiene as well as vaccination, whereby only protection rates of 50-70 % are achieved by currently available vaccines. In the light of increasing multi-drug resistance, a more effective conjugate vaccine against Salmonella Typhi with cross-reactivity against Salmonella Paratyphi is needed more than ever.

Travel-Related Typhoid Fever: Narrative Review of the Scientific Literature.

Enteric fever is a foodborne infectious disease caused by Salmonella enterica serotypes Typhi and Paratyphi A, B and C. The high incidence in low income countries can increase the risk of disease in travelers coming from high income countries. Pre-travel health advice on hygiene and sanitation practices and vaccines can significantly reduce the risk of acquiring infections. Although the majority of the cases are self-limiting, life-threatening complications can occur. Delayed diagnosis and cases of infections caused by multi-drug resistant strains can complicate the clinical management and affect the prognosis. More international efforts are needed to reduce the burden of disease in low income countries, indirectly reducing the risk of travelers in endemic settings. Surveillance activities can help monitor the epidemiology of cases caused by drug-susceptible and resistant strains.

Salmonella enterica serovar Paratyphi A isolated from a hard-to-heal diabetic ulcer: a case report.

Chronically infected diabetic wounds have a polymicrobial aetiology. However, Salmonella Paratyphi A is a very rare cause of wound infection. A 76-year-old female patient with type II diabetes presented with a wound on the left leg of two months' duration. The wound was painful, erythematous and a thick, foul-smelling discharge was present. There was a history of delayed wound healing. Salmonella Paratyphi A and Pseudomonas aeruginosa were isolated from the wound tissue. The patient was treated with cefuroxime and cloxacillin empirically and following the antibiotic susceptibility testing (ABST) report, ciprofloxacin was given for 10 days. The wound was treated with multiple debridements and topical antiseptic. On follow-up, the patient remained afebrile with subsiding discharge from the ulcer. This is the first reported case of Salmonella Paratyphi A from an infected diabetic ulcer in Sri Lanka and it serves to further define the spectrum of illnesses caused by this uncommon pathogen.

Use of pefloxacin as a surrogate marker to detect ciprofloxacin susceptibility in Salmonella enterica serotypes Typhi and Paratyphi A.

OBJECTIVE: To determine the use of pefloxacin as a surrogate marker to detect fluoroquinolone (ciprofloxacin) susceptibility against Salmonella enterica serotypes Typhi and Paratyphi A. METHODS: The prospective, descriptive cross-sectional study was conducted at the Aga Khan University Hospital, Karachi, from September 2016 to March 2018, and comprised Salmonella Typhi and Paratyphi A isolates of blood cultures. Disk susceptibility tests and broth microdilution to test minimum inhibitory concentration were performed as per standard guidelines. Data was analysed using SPSS 21. RESULTS: Of the 138 isolates, 91(66%) were intermediate resistant to ciprofloxacin but were resistant to pefloxacin, 42(30%) were resistant to both ciprofloxacin and pefloxacin, and 5(4%) were susceptible to both ciprofloxacin and pefloxacin. Of the isolates that were intermediate resistant to ciprofloxacin, 85(93%) had minimum inhibitory concentration range0.12-0.5mg\L, while 6(7%) had MIC>1mg\L (p<0.0001). CONCLUSIONS: Pefloxacin disk diffusion test was found to be reliable in detecting fluoroquinolone resistance among enteric fever causing Salmonella.

Genomic surveillance detects Salmonella enterica serovar Paratyphi A harbouring blaCTX-M-15 from a traveller returning from Bangladesh.

Whole genome sequencing (WGS) has been used routinely by Public Health England (PHE) for identification, surveillance and monitoring of resistance determinants in referred Salmonella isolates since 2015. We report the first identified case of extended-spectrum-ß-lactamase (ESBL) Salmonella enterica serovar Paratyphi A (S. Paratyphi A) isolated from a traveller returning to England from Bangladesh in November 2017. The isolate (440915) was resistant to ciprofloxacin and harboured both the mobile element ISEcp9 -blaCTX-M-15-hp-tnpA and blaTEM-191, associated with ESBL production. Phenotypic resistance was subsequently confirmed by Antimicrobial Susceptibility Testing (AST). S. Paratyphi A 440915 harboured an IncI1 plasmid previously reported to encode ESBL elements in Enterobacteriaceae and recently described in a S. Typhi isolate from Bangladesh. Results from this study indicate the importance of monitoring imported drug resistance for typhoidal salmonellae as ceftriaxone is the first line antibiotic treatment for complicated enteric fever in England. We conclude that WGS provides a rapid, accurate method for surveillance of drug resistance genes in Salmonella, leading to the first reported case of ESBL producing S. Paratyphi A and continues to inform the national treatment guidelines for management of enteric fever.

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.

Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance.

BACKGROUND: With the rise in fluoroquinolone-resistant Salmonella Typhi and the recent emergence of ceftriaxone resistance, azithromycin is one of the last oral drugs available against typhoid for which resistance is uncommon. Its increasing use, specifically in light of the ongoing outbreak of extensively drug-resistant (XDR) Salmonella Typhi (resistant to chloramphenicol, ampicillin, cotrimoxazole, streptomycin, fluoroquinolones and third-generation cephalosporins) in Pakistan, places selective pressure for the emergence and spread of azithromycin-resistant isolates. However, little is known about azithromycin resistance in Salmonella, and no molecular data are available on its mechanism. METHODS AND FINDINGS: We conducted typhoid surveillance in the two largest pediatric hospitals of Bangladesh from 2009-2016. All typhoidal Salmonella strains were screened for azithromycin resistance using disc diffusion and resistance was confirmed using E-tests. In total, we identified 1,082 Salmonella Typhi and Paratyphi A strains; among these, 13 strains (12 Typhi, 1 Paratyphi A) were azithromycin-resistant (MIC range: 32-64 µg/ml) with the first case observed in 2013. We sequenced the resistant strains, but no molecular basis of macrolide resistance was identified by the currently available antimicrobial resistance prediction tools. A whole genome SNP tree, made using RAxML, showed that the 12 Typhi resistant strains clustered together within the 4.3.1.1 sub-clade (H58 lineage 1). We found a non-synonymous single-point mutation exclusively in these 12 strains in the gene encoding AcrB, an efflux pump that removes small molecules from bacterial cells. The mutation changed the conserved amino acid arginine (R) at position 717 to a glutamine (Q). To test the role of R717Q present in azithromycin-resistant strains, we cloned acrB from azithromycin-resistant and sensitive strains, expressed them in E. coli, Typhi and Paratyphi A strains and tested their azithromycin susceptibility. Expression of AcrB-R717Q in E. coli and Typhi strains increased the minimum inhibitory concentration (MIC) for azithromycin by 11- and 3-fold respectively. The azithromycin-resistant Paratyphi A strain also contained a mutation at R717 (R717L), whose introduction in E. coli and Paratyphi A strains increased MIC by 7- and 3-fold respectively, confirming the role of R717 mutations in conferring azithromycin resistance. CONCLUSIONS: This report confirms 12 azithromycin-resistant Salmonella Typhi strains and one Paratyphi A strain. The molecular basis of this resistance is one mutation in the AcrB protein at position 717. This is the first report demonstrating the impact of this non-synonymous mutation in conferring macrolide resistance in a clinical setting. With increasing azithromycin use, strains with R717 mutations may spread and be acquired by XDR strains. An azithromycin-resistant XDR strain would shift enteric fever treatment from outpatient departments, where patients are currently treated with oral azithromycin, to inpatient departments to be treated with injectable antibiotics like carbapenems, thereby further burdening already struggling health systems in endemic regions. Moreover, with the dearth of novel antimicrobials in the horizon, we risk losing our primary defense against widespread mortality from typhoid. In addition to rolling out the WHO prequalified typhoid conjugate vaccine in endemic areas to decrease the risk of pan-resistant Salmonella Typhi strains, it is also imperative to implement antimicrobial stewardship and water sanitation and hygiene intervention to decrease the overall burden of enteric fever.

Chemical composition, antibacterial activity and related mechanism of valonia and shell from Quercus variabilis Blume (Fagaceae) against Salmonella paratyphi a and Staphylococcus aureus.

BACKGROUND: Plant secondary metabolites and phytochemicals that exhibit strong bioactivities have potential to be developed as safe and efficient natural antimicrobials against food contamination and addressing antimicrobial resistance caused by the overuse of chemical synthetic preservative. In this study, the chemical composition, antibacterial activities and related mechanism of the extracts of the valonia and the shell of Quercus variabilis Blume were studied to determine its potential as a safe and efficient natural antimicrobial. METHODS: The phenolic compositions of valonia and shell extracts were determined by folin-ciocalteau colourimetric method, sodium borohydride/chloranil-based assay and the aluminium chloride method and then further identified by the reverse-phase HPLC analysis. The antibacterial activities of valonia and shell extracts were evaluated by the agar disk diffusion method and agar dilution method. The related antibacterial mechanism was explored successively by the membrane of pathogens effect, phosphorous metabolism, whole-cell proteins and the microbial morphology under scanning electron microscopy. RESULTS: The n-butanol fraction and water fraction of valonia along with n-butanol fraction of the shell contains enrich phenolics including ellagic acid, theophylline, caffeic acid and tannin acid. The n-butanol fraction and ethanol crude extracts of valonia exhibited strong antibacterial activities against Salmonella paratyphi A (S. paratyphi A) and Staphylococcus aureus (S. aureus) with the DIZ values ranged from 10.89 ± 0.12 to 15.92 ± 0.44, which were greater than that of the Punica granatum (DIZ: 10.22 ± 0.18 and 10.30 ± 0.21). The MIC values of the n-butanol fraction and ethanol crude extracts of valonia against S. paratyphi A and S. aureus were 1.25 mg/ml and 0.625 mg/ml. The related antibacterial mechanism of n-butanol fraction and ethanol crude extracts of valonia may be attributed to their strong impact on membrane permeability and cellular metabolism. Those extracts exhibited strong antibacterial activity according to inhibit the synthesis of bacterial proteins and seriously change morphological structure of bacterial cells. CONCLUSIONS: The n-butanol fraction and ethanol crude extracts of valonia had reasonably good antibacterial activities against S. paratyphi A and S. aureus. This study suggests possible application of valonia and shell as natural antimicrobials or preservatives for food and medical application.

Synthesis of new multivalent metal ion functionalized mesoporous silica and studies of their enhanced antimicrobial and cytotoxicity activities.

In the present study, we have reported the synthesis of a transition metal (Me = Ti, V, and Pd) incorporated into MCM-41 mesoporous molecular sieves (Si/Me = 20) synthesized by the sol-gel method. Their physicochemical properties were studied in detail by standard techniques like low angle powder X-ray diffraction (XRD), scanning electron microscopy-energy-dispersive X-ray spectroscopy (SEM-EDXS), transmission electron microscopy (TEM), N2 adsorption/desorption studies, and thermogravimetric-differential thermal (TG-DTA) analysis and spectral studies like Fourier transform infrared spectroscopic analysis (FT-IR), diffuse reflectance ultraviolet-visible spectroscopic analysis (UV-Visible-DRS), and X-ray photoelectron spectroscopy (XPS). The XRD patterns prove that the material's phase identity is the same irrespective of metal incorporation. SEM displayed the uniform shape and size of the nanoparticles. The presence of elements such as Ti, V, Pd, Si and O in respective materials is revealed using the EDXS analysis. Around 30% weight loss arose upon calcination from room temperature to 800 °C. BET surface area analysis presented that the parent materials have a high surface area (1024 m2 g-1) which was reduced upon metal incorporation. FT-IR analysis exhibited the framework vibrations of the synthesised materials. UV-Visible-DRS analysis indicated the presence of tetrahedrally coordinated transition metal ions. The multivalent-metal-ion-functionalized mesoporous materials showed significant enhancement in potent antimicrobial and anticancer activity. The antimicrobial activity is because of its low lipophilicity, which no longer allows the materials to enter via the lipid membrane. Thus, the new materials neither obstruct the metal-binding sites nor inhibit the growth of microbe enzymes. Further, the results show that the transition metal ion-containing mesoporous materials possessing good anticancer activity arising from their excessive surface area to volume ratio provided appropriate association with a tumour cell due to the direct penetration of mesoporous materials into the cell wall, causing membrane damage and cell death.

Spatial and Temporal Patterns of Typhoid and Paratyphoid Fever Outbreaks: A Worldwide Review, 1990-2018.

BACKGROUND: Analyses of the global spatial and temporal distribution of enteric fever outbreaks worldwide are important factors to consider in estimating the disease burden of enteric fever disease burden. METHODS: We conducted a global literature review of enteric fever outbreak data by systematically using multiple databases from 1 January 1990 to 31 December 2018 and classified them by time, place, diagnostic methods, and drug susceptibility, to illustrate outbreak characteristics including spatial and temporal patterns. RESULTS: There were 180 940 cases in 303 identified outbreaks caused by infection with Salmonella enterica serovar Typhi (S. Typhi) and Salmonella enterica serovar Paratyphi A or B (S. Paratyphi). The size of outbreak ranged from 1 to 42 564. Fifty-one percent of outbreaks occurred in Asia, 15% in Africa, 14% in Oceania, and the rest in other regions. Forty-six percent of outbreaks specified confirmation by blood culture, and 82 outbreaks reported drug susceptibility, of which 54% had multidrug-resistant pathogens. Paratyphoid outbreaks were less common compared to typhoid (22 vs 281) and more prevalent in Asia than Africa. Risk factors were multifactorial, with contaminated water being the main factor. CONCLUSIONS: Enteric fever outbreak burden remains high in endemic low- and middle-income countries and, despite its limitations, outbreak data provide valuable contemporary evidence in prioritizing resources, public health policies, and actions. This review highlights geographical locations where urgent attention is needed for enteric fever control and calls for global action to prevent and contain outbreaks.

Draft genome of a macrolide resistant XDR Salmonella enterica serovar Paratyphi A strain using a shotgun sequencing approach.

OBJECTIVES: Salmonella enterica serovar Paratyphi A, the causative pathogen of enteric fever, is a major public-health concern affecting millions of people around the world. We conducted whole-genome sequencing and analysis of a novel macrolide-resistant Salmonella Paratyphi A strain isolated from Karachi, Pakistan. METHODS: Genomic DNA of Salmonella Paratyphi A strain JRCGR-AK14 was sequenced on a MiSeq platform. Read quality was evaluated and paired-end reads were assembled into contigs and scaffolds. The quality of contigs and scaffolds was evaluated and assembled contigs were annotated. Virulence genes, antimicrobial resistance genes (ARGs), tRNAs, rRNAs, coding sequences and clustered regularly interspaced short palindromic repeats (CRISPRs) were identified. ARGs and mutations in quinolone-resistance determining regions (QRDRs) were identified by Antimicrobial Resistance Identification By Assembly (ARIBA) and ResFinder. Known and unknow mutations in the QRDRs were predicted. RESULTS: The genome of Salmonella Paratyphi A was calculated at 4529866 bp with 4381 genes and 1088 hypothetical proteins. Several putative genes coding for multidrug efflux pumps were identified. In addition, gene mutations conferring resistance to nitrofurantoin (e.g. marA, mdsC, Escherichia coli soxS), pulvomycin (e.g. H-NS, cpxA, E. coli EF-Tu) and fosfomycin (CRP, kdpE, E. coli glpT) were also identified. Several ARGs along with the mobile genetic element transposon Tn10 were also identified. It is evident from the results that diverse redundant mechanisms are involved in regulation of drug resistance in this strain. CONCLUSION: The current findings provide valuable data for understanding the multidrug resistance and pathogenic characteristics of clinical Salmonella Paratyphi A isolates.

Typhoidal Salmonella strains in Pakistan: an impending threat of extensively drug-resistant Salmonella Typhi.

The aim of this study is to see the frequency, clinical presentation, and therapeutic response of extensively drug-resistant Salmonella enterica serovar Typhi and current susceptibility pattern of typhoidal Salmonella strains in our setup. This study was carried out at the Department of Medical Microbiology and Immunology and Department of Medicine, Pakistan Navy Ship (PNS) Shifa Hospital, Karachi, from January 1 to December 31, 2018. All the blood culture samples of patients (indoor and outdoor) with suspicion of enteric fever were processed. Isolates were cultured and identified using standard microbiological procedures. The antimicrobial sensitivity against the typhoidal Salmonellae was determined using Kirby-Bauer disc diffusion method as per the guidelines of Clinical and Laboratory Standards Institute (2018) and all the extensively drug-resistant (XDR) isolates were confirmed by Vitek 2 system. Clinical presentation and response to treatment of patients were followed. A total of 292 typhoidal Salmonella isolates were cultured. Resistance to ciprofloxacin against both Salmonella Typhi and Salmonella Paratyphi A was found to be very high (91%). Percentage of multidrug-resistant (MDR) isolates in Salmonella Typhi was 76% (182 isolates) and in Salmonella Paratyphi it was 34% (18 isolates). XDR isolates in Salmonella Typhi were significant that is 48% (115 isolates). Only 10 cases were given azithromycin who responded to treatment in mean 4.3 days. Out of 115 cases of XDR Salmonella Typhi, 103 patients were given parenteral meropenem and clinical response was seen in mean 5 days. The emergence and rapid spread of extensively drug-resistant Salmonella Typhi is alarming and highlights the significance of strict antimicrobial susceptibility surveillance programs with antimicrobial stewardship.

Molecular mechanisms of antimicrobial resistance and phylogenetic relationships of Salmonella enterica isolates from febrile patients in Yangon, Myanmar.

BACKGROUND: Enteric fever is common in southeast Asia. However, there is little information on the circulating Salmonella enterica strains causing enteric fever in Myanmar. METHODS: We performed antimicrobial susceptibility testing and whole genome sequencing on S. enterica bloodstream isolates from febrile patients aged ≥12 y attending two hospitals in Yangon, Myanmar, from 5 October 2015 through 4 October 2016. We identified the serovar of S. enterica, determined antimicrobial susceptibility and the molecular mechanisms of resistance. We analysed phylogenetic relationships among Myanmar S. enterica isolates and those with isolates from neighbouring countries. RESULTS: Of 73 S. enterica isolated, 39 (53%) were serovar Typhi and 34 (47%) were Paratyphi A. All isolates were susceptible to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole but resistant to ciprofloxacin. We identified mutations in chromosomal genes gyrA, gyrB and parC as responsible for fluoroquinolone resistance. All S. enterica Typhi isolates were of 4.3.1 subclade (formerly known as H58) and formed two closely related genotypic clusters; both clusters were most closely related to isolates from India from 2012. All S. enterica Paratyphi A were lineage C, clade C4 and were closely related. CONCLUSION: Our study describes currently circulating S. enterica serovars in Myanmar, the genetic basis of their antimicrobial resistance and provides a genotypic framework for epidemiologic study.

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.