A systematic review of antimicrobial resistance of typhoidal Salmonella in India

Trends in antimicrobial susceptibility pattern of Salmonella species isolated from bacteremia patients at a tertiary care center in Northern India

The study was done to assess the antimicrobial susceptibility pattern among Salmonella enterica serovars causing bacteremia in Northern India. In this observational study, blood samples positive for Salmonella enterica serovars from January 2021 to April 2023 were studied. Species identification was done using MALDI-ToF MS. Serotyping was done using slide agglutination method. Antimicrobial susceptibility was interpreted as per the CLSI guidelines. During the study period, 32 Salmonella enterica serovars were isolated. Salmonella enterica serovar Typhi was the predominant serovar, followed by Salmonella enterica serovar Paratyphi A. All isolates were susceptible to ceftriaxone, chloramphenicol, co-trimoxazole and cefotaxime. Pefloxacin showed 100% resistance. Resistance to nalidixic acid was found in 81.2% isolates. Of the isolates resistant to nalidixic acid, 19(73.08%) isolates were resistant to ciprofloxacin also. This changing susceptibility pattern necessitates continuous surveillance of antibiogram of Salmonella isolates to rationalize the treatment protocols for invasive salmonellosis and prevent emergence of resistant strains.

Tackling salmonellosis: A comprehensive exploration of risks factors, impacts, and solutions

Salmonellosis, caused by Salmonella species, is one of the most common foodborne illnesses worldwide with an estimated 93.8 million cases and about 155,00 fatalities. In both industrialized and developing nations, Salmonellosis has been reported to be one of the most prevalent foodborne zoonoses and is linked with arrays of illness syndromes such as acute and chronic enteritis, and septicaemia. The two major and most common Salmonella species implicated in both warm-blooded and cold-blooded animals are Salmonella bongori and Salmonella enterica. To date, more than 2400 S. enterica serovars which affect both humans and animals have been identified. Salmonella is further classified into serotypes based on three primary antigenic determinants: somatic (O), flagella (H), and capsular (K). The capacity of nearly all Salmonella species to infect, multiply, and survive in human host cells with the aid of their pathogenic and virulence arsenals makes them deadly and important public health pathogens. Primarily, food-producing animals such as poultry, swine, cattle, and their products have been identified as important sources of salmonellosis. Additionally, raw fruits and vegetables are among other food types that have been linked to the spread of Salmonella spp. Based on the clinical manifestation of human salmonellosis, Salmonella strains can be categorized as either non-typhoidal Salmonella (NTS) and typhoidal Salmonella. The detection of aseptically collected Salmonella in necropsies, environmental samples, feedstuffs, rectal swabs, and food products serves as the basis for diagnosis. In developing nations, typhoid fever due to Salmonella Typhi typically results in the death of 5%-30% of those affected. The World Health Organization (WHO) calculated that there are between 16 and 17 million typhoid cases worldwide each year, with scaring 600,000 deaths as a result. The contagiousness of a Salmonella outbreak depends on the bacterial strain, serovar, growth environment, and host susceptibility. Risk factors for Salmonella infection include a variety of foods; for example, contaminated chicken, beef, and pork. Globally, there is a growing incidence and emergence of life-threatening clinical cases, especially due to multidrug-resistant (MDR) Salmonella spp, including strains exhibiting resistance to important antimicrobials such as beta-lactams, fluoroquinolones, and third-generation cephalosporins. In extreme cases, especially in situations involving very difficult-to-treat strains, death usually results. The severity of the infections resulting from Salmonella pathogens is dependent on the serovar type, host susceptibility, the type of bacterial strains, and growth environment. This review therefore aims to detail the nomenclature, etiology, history, pathogenesis, reservoir, clinical manifestations, diagnosis, epidemiology, transmission, risk factors, antimicrobial resistance, public health importance, economic impact, treatment, and control of salmonellosis.

A study of antibiotic resistance pattern of clinical bacterial pathogens isolated from patients in a tertiary care hospital

We investigated antibiotic resistance pattern in clinical bacterial pathogens isolated from in-patients and out-patients, and compared it with non-clinical bacterial isolates. 475 bacterial strains isolated from patients were examined for antibiotic resistance. Staphylococcus spp. (148; 31.1%) were found to be the most prevalent, followed by Klebsiella pneumoniae (135; 28.4%), Escherichia coli (74; 15.5%), Pseudomonas aeruginosa (65; 13.6%), Enterobacter spp. (28; 5.8%), and Acinetobacter spp. (25; 5.2%). Drug-resistant bacteria isolated were extended spectrum-β-lactamase K. pneumoniae (8.8%), E. coli (20%), metallo-β-lactamase P. aeruginosa (14; 2.9%), erythromycin-inducing clindamycin resistant (7.4%), and methicillin-resistant Staphylococcus species (21.6%). Pathogens belonging to the Enterobacteriaceae family were observed to undergo directional selection developing resistance against antibiotics ciprofloxacin, piperacillin-tazobactam, cefepime, and cefuroxime. Pathogens in the surgical ward exhibited higher levels of antibiotic resistance, while non-clinical P. aeruginosa and K. pneumoniae strains were more antibiotic-susceptible. Our research assisted in identifying the drugs that can be used to control infections caused by antimicrobial resistant bacteria in the population and in monitoring the prevalence of drug-resistant bacterial pathogens.

Genomic Investigation of Salmonella Typhi in Hong Kong Revealing the Predominance of Genotype 3.2.2 and the First Case of an Extensively Drug-Resistant H58 Genotype

Typhoid fever is a notable disease in Hong Kong. We noticed two local cases of typhoid fever caused by Salmonella Typhi within a two-week period in late 2022, which had no apparent epidemiological linkage except for residing in the same region of Hong Kong. A phylogenetic study of Salmonella Typhi isolates from Hong Kong Island from 2020 to 2022 was performed, including a whole-genome analysis, the typing of plasmids, and the analysis of antibiotic-resistance genes (ARGs), to identify the dominant circulating strain and the spread of ARGs. A total of seven isolates, from six local cases and an imported case, were identified from positive blood cultures in two hospitals in Hong Kong. Five antibiotic-sensitive strains of genotype 3.2.2 were found, which clustered with another 30 strains originating from Southeast Asia. Whole-genome sequencing revealed clonal transmission between the two index cases. The remaining two local cases belong to genotype 2.3.4 and genotype 4.3.1.1.P1 (also known as the H58 lineage). The genotype 4.3.1.1.P1 strain has an extensively drug-resistant (XDR) phenotype (co-resistance to ampicillin, chloramphenicol, ceftriaxone, ciprofloxacin, and co-trimoxazole). Although the majority of local strains belong to the non-H58 genotype 3.2.2 with a low degree of antibiotic resistance, the introduction of XDR strains with the global dissemination of the H58 lineage remains a concern.

Controlling of Bacterial Virulence: Evaluation of Anti-Virulence Activities of Prazosin against Salmonella enterica

Salmonella enterica is a Gram-negative orofecal transmitted pathogen that causes a wide diversity of local and systemic illnesses. Salmonella enterica utilizes several interplayed systems to regulate its invasion and pathogenesis: namely, quorum sensing (QS) and type three secretion system (T3SS). In addition, S. enterica could sense the adrenergic hormones in the surroundings that enhance its virulence. The current study aimed to evaluate the ability of α-adrenoreceptor antagonist prazosin to mitigate the virulence of S. enterica serovar Typhimurium. The prazosin effect on biofilm formation and the expression of sdiA, qseC, qseE, and T3SS-type II encoding genes was evaluated. Furthermore, the prazosin intracellular replication inside macrophage and anti-virulence activity was evaluated in vivo against S. typhimurium. The current finding showed a marked prazosin ability to compete on SdiA and QseC and downregulate their encoding genes. Prazosin significantly downregulated the virulence factors encoding genes and diminished the biofilm formation, intracellular replication inside macrophages, and in vivo protected mice. To sum up, prazosin showed significant inhibitory activities against QS, T3SS, and bacterial espionage, which documents its considered anti-virulence activities.

Quantifying antibiotic use in typhoid fever in India: a cross-sectional analysis of private sector medical audit data, 2013-2015

OBJECTIVES

To estimate the antibiotic prescription rates for typhoid in India.

DESIGN

Cross-sectional study.

SETTING

Private sector primary care clinicians in India.

PARTICIPANTS

The data came from prescriptions of a panel of 4600 private sector primary care clinicians selected through a multistage stratified random sampling accounting for the region, specialty type and patient turnover. The data had 671 million prescriptions for antibiotics extracted from the IQVIA database for the years 2013, 2014 and 2015.

PRIMARY AND SECONDARY OUTCOME MEASURES

Mean annual antibiotic prescription rates; sex-specific and age-specific prescription rates; distribution of antibiotic class.

RESULTS

There were 8.98 million antibiotic prescriptions per year for typhoid, accounting for 714 prescriptions per 100 000 population. Children 10-19 years of age represented 18.6% of the total burden in the country in absolute numbers, 20-29 year age group had the highest age-specific rate, and males had a higher average rate (844/100 000) compared with females (627/100 000). Ten different antibiotics accounted for 72.4% of all prescriptions. Cefixime-ofloxacin combination was the preferred drug of choice for typhoid across all regions except the south. Combination antibiotics are the preferred choice of prescribers for adult patients, while cephalosporins are the preferred choice for children and young age. Quinolones were prescribed as monotherapy in 23.0% of cases.

CONCLUSIONS

Nationally representative private sector antibiotic prescription data during 2013-2015 indicate a higher disease burden of typhoid in India than previously estimated. The total prescription rate shows a declining trend. Young adult patients account for close to one-third of the cases and children less than 10 years account for more than a million cases annually.

Clinical Characteristics and Antibiotics Sensitivity of Culture Positive Typhoid Fever Patients in Baghdad Teaching Hospital - A Single Center Study

BACKGROUND: Enteric fever caused by Salmonella Typhi is an endemic disease in Iraq. Variations in presentations make it a diagnostic challenge. If untreated or treated inappropriately then it is a serious disease with potentially life-threatening complications. The recent emergence of drug resistant strains of S. Typhi is a rising public health problem and a clinical concern to the physician. AIM: The objectives of the study were to assess and describe the patterns of antimicrobial resistance, clinical characteristics, epidemiological distribution, and complications of typhoid fever. PATIENTS AND METHODS: Fifty cases of typhoid fever (culture proven) were collected during the period from February 2019 to November 2019 in the medical wards of Baghdad Teaching Hospital. Detailed history, physical examination, and laboratory investigations were conducted and statistical analysis of the results was done, prospective observational study was conducted. RESULTS: During the study period, 50 cases of typhoid fever were documented, mean age of presentation was 30.7 ± 12.8, 60% of the cases were male gender, gastrointestinal complications were the most common (90%) followed by hematological complications (71%). Mortality of typhoid fever in our study was 2%. High percentage of resistance to third generation cephalosporins, ciprofloxacin, and azithromycin was found (96%, 56%, and 56%, respectively) while good sensitivity to trimethoprim and meropenem was found (94% and 76%, respectively). Significant association was also found between the development of typhoid fever complications and the presence of anemia, thrombocytopenia, lymphopenia, and eosinopenia. Significant association was also found between the complications and the infection with strains resistant to cephalosporins, ciprofloxacin, and azithromycin. CONCLUSIONS: There is a concerning increase in resistance toward cephalosporins, ciprofloxacin, and azithromycin while meropenem and trimethoprim are emerging as effective drugs. There was high incidence of complications found (84%).Lymphopenia, anemia, eosinopenia, and thrombocytopenia are independent risk factors for the development of complications of typhoid fever.

Antimicrobial Resistance: The 'Other' Pandemic! : Based on 9th Dr. I. C. Verma Excellence Award for Young Pediatricians Delivered as Oration on 19th Sept. 2021

Antimicrobial resistance is projected to kill 10 million people by 2050. The biggest driver of antimicrobial resistance is excessive/unrestricted use of antimicrobials in humans and animals. Antimicrobial resistance is a problem in all types of pathogens including bacteria, mycobacteria, viruses, fungi, and parasites both globally and India and in both adults and children. The areas of greatest concern for India is the epidemic of MDR and XDR tuberculosis and resistance in gram-negative pathogens. The alarming rate of extended spectrum beta lactamase (ESBL) production in Enterobacteriales in both community and health care-associated infections is driving carbapenem use. Rates of carbapenem resistance are now significantly high in health care-associated gram negative pathogens with associated high mortality rates. The key solution to this antimicrobial resistance crisis needs participation of all stakeholders and lies in promoting rational antimicrobial therapy.

Characterisation of Salmonella Enteritidis ST11 and ST1925 Associated with Human Intestinal and Extra-Intestinal Infections in Singapore

Salmonella Enteritidis is a major foodborne pathogen worldwide. In this study, a total of 276 S. enteritidis isolates, collected between 2016 and 2017 from human, food and farm/slaughterhouse samples, were studied to enhance the understanding of the epidemiology of human salmonellosis in Singapore. Results showed all 276 isolates belonged either to ST1925 (70.3%) or ST11 (29.7%), with ST11 being significantly more frequent in extra-intestinal isolates and chicken isolates. Food isolates, most of which were from poultry, showed the highest prevalence of resistance (33–37%) against beta-lactams or beta-lactams/beta-lactamase inhibitor combination (ampicillin, piperacillin and ampicillin/sulbactam). The analysis showed the detection of genes associated with resistance to aminoglycoside genes (99.6%), tetracycline (55.1%), and beta-lactams (14.9%) of all isolates. Nine types of plasmids were found in 266 isolates; the most common incompatibility group profiles were IncFIB(S)-IncFII(S)-IncX1 (72.2%) and IncFIB(S)-IncFII(S) (15.8%). Most plasmid harbouring isolates from chicken (63.6%, 14/22) and from human (73.8%, 175/237) shared the same plasmid profile (IncFIB(S)-IncFII(S)-IncX1). SNP analysis showed clustering of several isolates from poultry food products and human isolates, suggesting phylogenetic relatedness among these isolates. Lastly, this study provides important epidemiological insights on the application of phenotypic and next-generation sequencing (NGS) tools for improved food safety and public health surveillance and outbreak investigation of S.enteritidis.

Phenotypic Detection of ESBL, AmpC, MBL, and Their Co-occurrence among MDR Enterobacteriaceae Isolates in a Tertiary Care Hospital in Sikkim, India

Background Emergence of extended-spectrum beta-lactamases (ESBLs), AmpC β-lactamases, and metallo-β lactamases (MBL), and their co-existence among members of Enterobacteriaceae pose newer diagnostic and therapeutic challenges. The present study examines the ESBL, AmpC, and MBL production by various phenotypic methods and their co-occurrence among the multidrug-resistant (MDR) Enterobacteriaceae clinical isolates.

Materials and Methods Four hundred non-repetitive Enterobacteriaceae clinical isolates were collected from the Central Referral Hospital, Sikkim. The isolates were used for identification and their antibiotic susceptibility tests were performed according to the Clinical and Laboratory Standard Institute (CLSI) guidelines. ESBL was detected by double-disc synergy test (DDST) and phenotypic confirmatory disc-diffusion test (PCDDT), AmpC detection by AmpC E-test, and boronic acid disc diffusion (BD) test. MBL was detected using the imipenem–imipenem/EDTA disc and carba-NP tests.

Results Around 76% were considered MDR. ESBL was seen in 58% and 50.4% based on DDST and phenotypic confirmation disc-diffusion test (PCDDT), respectively. AmpC was detected in 11.8% and 13.1% using a commercial E-test and boronic acid test, respectively. MBL were identified in 12.8% and 14.8% based on MBL imipenem-EDTA and carba-NP tests, respectively. Co-occurrence of ESBL and AmpC, ESBL and MBL, AmpC and MBL was seen in 5.2%, 11.5%, 1.3%, respectively, whereas a combination of these three β-lactamases was observed in only 0.3% of 304 MDR isolates.

Conclusion The findings highlight a high prevalence of β-lactamases and their co-production among the Enterobacteriaceae, mainly in Klebsiella pneumoniae and Escherichia coli isolates. The study further highlights the necessity to identify the MDR β-lactamases stains for effective therapy in severe as well as mild bacterial infections, thereby enabling to reduce the risk of MDR in hospital and community settings.

Multidrug-Resistant Infections in the Developing World

Antimicrobials are essential in reducing morbidity and mortality from infectious diseases globally. However, due to the lack of effective surveillance measures and widespread overuse, there is an increasing threat to the effectiveness of antimicrobials. Although there is a global increase in antimicrobial resistance, low- and middle-income countries share a much higher burden. Antimicrobial stewardship efforts such as effective surveillance and reduction in overuse can help combat the increase in antimicrobial resistance.

Assessment of rationality of available fixed dose combinations of antibiotics in India

OBJECTIVE

India is among the largest consumers of antibiotics. Easy availability and growing sales of Fixed Dose Combinations (FDCs) of antibiotics can worsen Antimicrobial Resistance (AMR). There is lack of comprehensive data on available antibiotic FDC formulations, their dose strengths and adequacy of scientific evidence regarding their efficacy, safety and suitability for human use. In the present work, we aimed at addressing this knowledge gap.

METHODS

Availability of FDCs was ascertained from the Current Index of Medical Specialties (CIMS) [Issue Jan-April 2020]. Customized data abstraction form was used to capture pertinent information for these FDCs. Assessment of rationality was done based on standard parameters.

RESULTS

More than 90% of the existing FDCs were found to be irrational; with two third of them being unapproved and or banned from use in the country.

CONCLUSIONS

Although the regulatory agency has already taken cognizance of the seriousness of the matter; there is an urgent need to revisit these FDCs to promote prudent antibiotic use.

EXPERT OPINION

High antibiotic use is associated with antimicrobial resistance; it is imperative that all factors which lead to high antibiotic use are adequately addressed. Easy availability of fixed dose combinations (FDCs) has begun to catch the attention of regulators in developing economies like India leading to a ban of 330 FDCs of which 19% were antibiotic combinations. The continuing presence and increasing sales of these irrational FDCs is a concern for effective antimicrobial stewardship.

Drivers of global media attention and representations for antimicrobial resistance risk: an analysis of online English and Chinese news media data, 2015-2018

BACKGROUND

How antimicrobial resistance (AMR) risk is communicated in news media can shape public understanding and the engagement of different sectors with AMR. This study examined online news media attention for AMR risk and analyzed how AMR risk was communicated using a global sample of English and Chinese news articles.

METHODS

A total of 16,265 and 8335 English and Chinese news relevant to AMR risk, respectively, published in 2015-2018 were retrieved from a professional media-monitoring platform, to examine media attention for AMR and its drivers, of which, 788 articles from six main English-speaking countries and three main Chinese-speaking territories were drawn using constructed-week sampling for content analysis.

RESULTS

Media attention mainly fluctuated around official reports or scientific discovery of AMR risks or solutions but seldom around reports of inappropriate antimicrobial use (AMU), and not consistently increased in response to World Antimicrobial Awareness Week. The content analysis found that (1) heterogeneous medical terminologies and the 'superbug' frame were most commonly used to define AMR or AMR risk; (2) a temporal increase in communicating microbial evolution as a process of AMR was identified but communication about inappropriate AMU in general consumers as the cause of AMR remained inadequate; and (3) the multifaceted consequences of AMR and individual actions that can be taken to tackle AMR were inadequately communicated.

CONCLUSIONS

The media should be encouraged or reoriented to communicate more about actions that can be taken by general consumers to enable collective actions and the multifaceted conseuqences of AMR to encourage one-health approach for tackling AMR.

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.

Using Weibo and WeChat social media channels to assess public awareness and practices related to antimicrobial resistance, China, 2019

Background

Antimicrobial resistance (AMR) is a global healthcare problem, including in China where high rates of resistance to common bacterial infections have been documented. In 2016, the National Health and Family Planning Commission (NHFPC) in China established a comprehensive strategic plan to increase awareness about AMR through education programs.

Methods

We conducted an online survey to assess changes in public knowledge, awareness and practices related to AMR in China since 2016. The survey was administered using China’s national and provincial level 12320 Health Hotline Weibo (micro-blog site) and WeChat (text messaging service) social media accounts from April 12, 2019 to May 7, 2019. All persons ≥16 years of age able to read Chinese were eligible to participate.

Results

A total of 2773 respondents completed the survey. Of the 2633 respondents indicating recent use of antibiotics, 84% (2223) reported obtaining their course of antibiotics from a hospital or pharmacy, 9% (246) of respondents reported using antibiotics saved from a previous prescription or treatment course, and 42% (1115) of respondents reported that they had stopped taking antibiotics as soon as they started feeling better. Most respondents correctly indicated that antibiotics can effectively treat urinary tract infections (86% [2388]) and skin infections (76% [2119]), but many incorrectly indicated that antibiotics can also treat viral infections such as measles (32% [889]) or a cold or flu (26% [726]). Of all respondents, 95% (2634) had heard of ‘antibiotic resistance’. Almost half (47% [1315]) reported using antibiotics within the last 6 months.

Conclusion

While awareness of AMR was high in this survey of social media users in China, inappropriate antibiotic use remains common, including the believe that antibiotics can effectively treat viral infections. Multiple interventions targeting the correct use of antibiotics and information on the cause AMR are likely needed. The 12320 Health Hotline provides a platform for conducting routine surveys to monitor antibiotic use and knowledge about AMR.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-021-10648-5.

Salmonella Typhi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance

Background

Recent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan. In India where typhoid fever is endemic, only sporadic cases of ceftriaxone resistant S. Typhi are reported. This study aimed at elucidating the phylogenetic evolutionary framework of ceftriaxone resistant S. Typhi isolates from India to predict their potential dissemination.

Methods

Five ceftriaxone resistant S. Typhi isolates from three tertiary care hospitals in India were sequenced on an Ion Torrent Personal Genome Machine (PGM). A core genome single-nucleotide-polymorphism (SNP) based phylogeny of the isolates in comparison to the global collection of MDR and XDR S. Typhi isolates was built. Two of five isolates were additionally sequenced using Oxford Nanopore MinION to completely characterize the plasmid and understand its transmission dynamics within Enterobacteriaceae.

Results

Comparative genomic analysis and detailed plasmid characterization indicate that while in Pakistan (4.3.1 lineage I) the XDR trait is associated with bla_CTX-M-15 gene on IncY plasmid, in India (4.3.1 lineage II), the ceftriaxone resistance is due to short term persistence of resistance plasmids such as IncX3 (bla_SHV-12) or IncN (bla_TEM-1B + bla_DHA-1).

Conclusion

Considering the selection pressure exerted by the extensive use of ceftriaxone in India, there are potential risks for the occurrence of plasmid transmission events in the predominant H58 lineages. Therefore, continuous monitoring of S. Typhi lineages carrying plasmid-mediated cephalosporin resistant genes is vital not just for India but also globally.

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S. Typhi to develop cephalosporin resistance by acquiring diverse plasmids from other Enterobacteriaceae.

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Independent acquisition of drug-resistant plasmids such as IncX3 and IncN with genes encoding beta-lactamases in H58 lineage II of S. Typhi.

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A short-term persistence of drug-resistant plasmids in H58 lineage II can be the reason for the sporadic cases cephalosporin resistant S. Typhi in India.

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Plasmid acquisition and maintenance of cephalosporin resistant S. Typhi appears to be specific to the phylogenetic lineage.

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Critical strategies in monitoring and control of cephalosporin resistant S. Typhi is needed to tackle further public health crisis.

Spontaneous Emergence of Azithromycin Resistance in Independent Lineages of Salmonella Typhi in Northern India

BACKGROUND

The emergence and spread of antimicrobial resistance (AMR) pose a major threat to the effective treatment and control of typhoid fever. The ongoing outbreak of extensively drug-resistant Salmonella Typhi (S. Typhi) in Pakistan has left azithromycin as the only remaining broadly efficacious oral antimicrobial for typhoid in South Asia. Ominously, azithromycin-resistant S. Typhi organisms have been subsequently reported in Bangladesh, Pakistan, and Nepal.

METHODS

Here, we aimed to understand the molecular basis of AMR in 66 S. Typhi organisms isolated in a cross-sectional study performed in a suburb of Chandigarh in Northern India using whole-genome sequencing and phylogenetic analysis.

RESULTS

We identified 7 S. Typhi organisms with the R717Q mutation in the acrB gene that was recently found to confer resistance to azithromycin in Bangladesh. Six out of the seven azithromycin-resistant S. Typhi isolates also exhibited triple mutations in gyrA (S83F and D87N) and parC (S80I) genes and were resistant to ciprofloxacin. These contemporary ciprofloxacin/azithromycin-resistant isolates were phylogenetically distinct from each other and from those reported from Bangladesh, Pakistan, and Nepal.

CONCLUSIONS

The independent emergence of azithromycin-resistant typhoid in Northern India reflects an emerging broader problem across South Asia and illustrates the urgent need for the introduction of typhoid conjugate vaccines in the region.

Tracking the Emergence of Azithromycin Resistance in Multiple Genotypes of Typhoidal Salmonella

The rising prevalence of antimicrobial resistance in Salmonella enterica serovars Typhi and Paratyphi A, causative agents of typhoid and paratyphoid, have led to fears of untreatable infections. Of specific concern is the emerging resistance against azithromycin, the only remaining oral drug to treat extensively drug resistant (XDR) typhoid. Since the first report of azithromycin resistance from Bangladesh in 2019, cases have been reported from Nepal, India, and Pakistan. The genetic basis of this resistance is a single point mutation in the efflux pump AcrB (R717Q/L). Here, we report 38 additional cases of azithromycin-resistant (AzmR) Salmonella Typhi and Paratyphi A isolated in Bangladesh between 2016 and 2018. Using genomic analysis of 56 AzmR isolates from South Asia with AcrB-R717Q/L, we confirm that this mutation has spontaneously emerged in different Salmonella Typhi and Paratyphi A genotypes. The largest cluster of AzmR Typhi belonged to genotype 4.3.1.1; Bayesian analysis predicts the mutation to have emerged sometime in 2010. A travel-related Typhi isolate with AcrB-R717Q belonging to 4.3.1.1 was isolated in the United Kingdom, increasing fears of global spread. For real-time detection of AcrB-R717Q/L, we developed an extraction-free, rapid, and low-cost mismatch amplification mutation assay (MAMA). Validation of MAMA using 113 AzmR and non-AzmR isolates yielded >98% specificity and sensitivity versus phenotypic and whole-genome sequencing assays currently used for azithromycin resistance detection. With increasing azithromycin use, AcrB-R717Q/L is likely to be acquired by XDR strains. The proposed tool for active detection and surveillance of this mutation may detect pan-oral drug resistance early, giving us a window to intervene.IMPORTANCE In the early 1900s, with mortality of ∼30%, typhoid and paratyphoid ravaged parts of the world; with improved water, sanitation, and hygiene in resource-rich countries and the advent of antimicrobials, mortality dwindled to <1%. Today, the burden rests disproportionately on South Asia, where the primary means for combatting the disease is antimicrobials. However, prevalence of antimicrobial resistance is rising and, in 2016, an extensively drug resistant Typhi strain triggered an ongoing outbreak in Pakistan, leaving only one oral drug, azithromycin, to treat it. Since the description of emergence of azithromycin resistance, conferred by a point mutation in acrB (AcrB-R717Q/L) in 2019, there have been increasing numbers of reports. Using genomics and Bayesian analysis, we illustrate that this mutation emerged in approximately 2010 and has spontaneously arisen multiple times. Emergence of pan-oral drug resistant Salmonella Typhi is imminent. We developed a low-cost, rapid PCR tool to facilitate real-time detection and prevention policies.

Susceptibility pattern of Salmonella enterica against commonly prescribed antibiotics, to febrile-pediatric cases, in low-income countries

BACKGROUND

In most low-income countries, febrile-pediatric-cases are often treated empirically with accessible antibiotics without periodic epidemiological surveillance, susceptibility testing, or minimal lethal dose calculations. With this backdrop, the study was undertaken to evaluate the susceptibility trend of Salmonella enterica against the commonly prescribed antibiotics.

METHODS

All isolates of Salmonella enterica were identified by standard protocols of biotyping and serotyping, then tested against antibiotics by the modified Kirby disk-diffusion method. Minimum Inhibitory Concentration (MIC) of isolates was determined by the agar-dilution method and compared with disk diffusion results and on nalidixic-acid sensitive/resistant strains.

RESULTS

Among 1815 febrile-pediatric patients, 90(4.9%) isolates of Salmonella enterica [serovar: Salmonella Typhi 62(68.8%) and Salmonella Paratyphi A 28(31.1%)] were recovered. The incidence of infection was higher among males, age groups 5 to 9, and patients enrolling in the out-patient department (OPD). On the disk-diffusion test, most isolates were sensitive against first-line drugs i.e.cephalosporins, and macrolides. However, against quinolones, a huge percentile 93.3%, of isolates were resistant [including 58 Typhiand 26 Paratyphiserovar] while nearly 14% were resistant against fluoroquinolones. When MICs breakpoint were adjusted as follows: 4 μg/ml for azithromycin, ≥1 μg/ml for ciprofloxacin, 2 μg/ml for ofloxacin, 8 μg/ml for nalidixic acid, and 1 μg/ml for cefixime, higher sensitivity and specificity achieved. Compared to other tested antibiotics, a low rate of azithromycin resistance was observed. Nevertheless, higher resistance against fluoroquinolones was observed on NARS strain.

CONCLUSION

Higher susceptibility of Salmonella enterica to the conventional anti-typhoidal drugs (amoxicillin, chloramphenicol, cotrimoxazole, cephotaxime) advocates for its reconsideration. Although, the lower susceptibility against fluoroquinolones among nalidixic-acid-resistant Salmonella (NARS) strain negates its empirical use among the study age group.

Syntheses of Salmonella Paratyphi A Associated Oligosaccharide Antigens and Development towards Anti-Paratyphoid Fever Vaccines

With the emergence of multidrug resistant Salmonella strains, the development of anti-Salmonella vaccines is an important task. Currently there are no approved vaccines against Salmonella Paratyphi A, the leading cause of paratyphoid fever. To fill this gap, oligosaccharides corresponding to the O-polysaccharide repeating units from the surface of Salmonella Paratyphi A have been synthesized through convergent stereoselective glycosylations. The synthetic glycan antigen was conjugated with a powerful immunogenic carrier system, the bacteriophage Qβ. The resulting construct was able to elicit strong and long-lasting anti-glycan IgG antibody responses, which were highly selective toward Salmonella Paratyphi A associated glycans. The availability of well-defined glycan antigen enabled the determination that one repeating unit of the polysaccharide is sufficient to induce protective antibodies, and the paratose residue and/or the O-acetyl modifications on the backbone are important for recognition by antibodies elicited by a Qβ-tetrasaccharide conjugate. Immune sera provided excellent protection to mice from lethal challenge with Salmonella Paratyphi A, highlighting the potential of the synthetic glycan-based vaccine.

Safety and immunogenicity of Vi-DT conjugate vaccine among 6-23-month-old children: Phase II, randomized, dose-scheduling, observer-blind Study

BACKGROUND

Typhoid causes significant mortality among young children in resource-limited settings. Conjugate typhoid vaccines could significantly reduce typhoid-related child deaths, but only one WHO-prequalified typhoid conjugate vaccine exists for young children. To address this gap, we investigated the safety, immunogenicity and dose-scheduling of Vi-DT typhoid conjugate vaccine among children aged 6-23 months.

METHODS

In this single center, observer blind, phase II trial, participants were randomly assigned (2:2:1) to receive one or two doses of Vi-DT or comparator vaccine. Anti-Vi IgG titer and geometric mean titers (GMT) were determined at 0, 4, 24 and 28 weeks. Data were analyzed using per-protocol and immunogenicity (a subset of intention-to-treat analysis) sets. The trial is registered with ClinicalTrials.gov (NCT03527355).

FINDINGS

Between April and July 2018, 285 children were randomized; 114 received one or two doses of Vi-DT while 57 received comparator. 277 completed the study follow-up per protocol; 112 and 110 from single- and two-dose Vi-DT schedules, respectively and 55 from the placebo group were included in the per protocol analysis. Safety profile is satisfactory. Thirteen serious adverse events were reported during the 28-week follow-up, none of which were related to Vi-DT. The seroconversion rate four weeks after the first dose was 100% (95% CI 98·3-100) in Vi-DT recipients and 7·0% (95% CI 2·8-16·7) in comparator recipients (p<0·0001). Similarly, the seroconversion rate 4 weeks after the second dose was 98·2% (95% CI 93· 6-99·5) and 21·8% (95% CI 13·0-34·4) among Vi-DT and comparator groups, respectively (p<0·0001). Anti-Vi IgG GMT was significantly higher in Vi-DT than in control group at all post-vaccination visits (p<0·0001).

INTERPRETATION

Both single and two doses of Vi-DT vaccine are safe, well tolerated, and immunogenic for infants and toddlers in a moderately endemic setting.

Genomic profiling of antimicrobial resistance genes in clinical isolates of Salmonella Typhi from patients infected with Typhoid fever in India

The development of multidrug resistance in Salmonella enterica serovar Typhi currently forms a major roadblock for the treatment of enteric fever. This poses a major health problem in endemic regions and extends to travellers returning from developing countries. The appearance of fluoroquinolone non-susceptible strains has resulted in use of ceftriaxone as drug of choice with azithromycin being recommended for uncomplicated cases of typhoid fever. A recent sporadic instance of decreased susceptibility to the latest drug regime has necessitated a detailed analysis of antimicrobial resistance genes and possible relationships with their phenotypes to facilitate selection of future treatment regimes. Whole genome sequencing (WGS) was conducted for 133 clinical isolates from typhoid patients. Sequence output files were processed for pan-genome analysis and prediction of antimicrobial resistance genes. The WGS analyses disclosed the existence of fluoroquinolone resistance conferring mutations in gyrA, gyrB, parC and parE genes of all strains. Acquired resistance determining mechanisms observed included catA1 genes for chloramphenicol resistance, dfrA7, dfrA15, sul1 and sul2 for trimethoprim-sulfamethoxazole and bla_TEM-116/bla_TEM-1B genes for amoxicillin. No resistance determinants were found for ceftriaxone and cefixime. The genotypes were further correlated with their respective phenotypes for chloramphenicol, ampicillin, co-trimoxazole, ciprofloxacin and ceftriaxone. A high correlation was observed between genotypes and phenotypes in isolates of S. Typhi. The pan-genome analysis revealed that core genes were enriched in metabolic functions and accessory genes were majorly implicated in pathogenesis and antimicrobial resistance. The pan-genome of S. Typhi appears to be closed (B_pan  =  0.09) as analysed by Heap’s law. Simpson’s diversity index of 0.51 showed a lower level of genetic diversity among isolates of S. Typhi. Overall, this study augments the present knowledge that WGS can help predict resistance genotypes and eventual correlation with phenotypes, enabling the chance to spot AMR determinants for fast diagnosis and prioritize antibiotic use directly from sequence.

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.

With the outbreak of extensively resistant (XDR) typhoid fever in Pakistan, azithromycin has become the last oral drug to treat typhoid. Although no azithromycin resistant XDR isolate has been reported to date, the increasing use of azithromycin and the clear historical record of widespread dissemination of resistance to all previously widely used antimicrobials by typhoidal Salmonella, suggest we will soon face strains resistant to all oral antibiotics. This makes it imperative to elucidate the mechanism of azithromycin resistance in typhoidal Salmonella. We tested 1,082 typhoidal Salmonella isolates from the two largest pediatric hospitals of Bangladesh and identified 13 azithromycin-resistant isolates. Using comparative genomics, we identified a mutation in a specific protein called AcrB that makes these isolates resistant to azithromycin. All azithromycin-resistant strains were susceptible to cephalosporin but resistant to all other oral antibiotics. The Pakistan outbreak strain is resistant to all common oral antibiotics and only susceptible to azithromycin. Acquisition of the plasmid that confers cephalosporin resistance in XDR strains by the Bangladeshi azithromycin-resistant strains or rise of the AcrB mutation in the XDR strains could be the end of oral treatment for typhoid. This poses serious threats to the health system of LMICs where typhoid is endemic. Currently, the majority of typhoid patients are prescribed oral treatment in the outpatient department, but an azithromycin-resistant XDR strain would shift enteric fever treatment from outpatient departments to inpatient departments to be treated with injectable antibiotics like carbapenems, 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 enteric fever.