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Salmonella Paratyphi A, one of the major etiologic agents of enteric fever, has increased in prevalence in recent decades in certain endemic regions in comparison to S. Typhi, the most prevalent cause of enteric fever. Despite this increase, data on the prevalence and molecular epidemiology of S. Paratyphi A remain generally scarce. Here, we analysed the whole genome sequences of 216 S. Paratyphi A isolates originating from Kathmandu, Nepal between 2005 and 2014, of which 200 were from patients with acute enteric fever and 16 from the gallbladder of people with suspected chronic carriage. By exploiting the recently developed genotyping framework for S. Paratyphi A (Paratype), we identified several genotypes circulating in Kathmandu. Notably, we observed an unusual clonal expansion of genotype 2.4.3 over a four-year period that spread geographically and systematically replaced other genotypes. This rapid genotype replacement is hypothesised to have been driven by both reduced susceptibility to fluoroquinolones and genetic changes to virulence factors, such as functional and structural genes encoding the type 3 secretion systems. Finally, we show that person-to-person is likely the most common mode of transmission and chronic carriers seem to play a limited role in maintaining disease circulation., Competing Interests: ‘The authors have declared that no competing interests exist.’, (Copyright: © 2024 Mylona et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: The proportion of enteric fever cases caused by Salmonella Paratyphi A is increasing and may increase further as we begin to introduce typhoid conjugate vaccines (TCVs). While numerous epidemiological and genomic studies have been conducted for S. Typhi, there are limited data describing the genomic epidemiology of S. Paratyphi A in especially in endemic settings, such as Bangladesh., Principal Findings: We conducted whole genome sequencing (WGS) of 67 S. Paratyphi A isolated between 2008 and 2018 from eight enteric disease surveillance sites across Bangladesh. We performed a detailed phylogenetic analysis of these sequence data incorporating sequences from 242 previously sequenced S. Paratyphi A isolates from a global collection and provided evidence of lineage migration from neighboring countries in South Asia. The data revealed that the majority of the Bangladeshi S. Paratyphi A isolates belonged to the dominant global lineage A (67.2%), while the remainder were either lineage C (19.4%) or F (13.4%). The population structure was relatively homogenous across the country as we did not find any significant lineage distributions between study sites inside or outside Dhaka. Our genomic data showed presence of single point mutations in gyrA gene either at codon 83 or 87 associated with decreased fluoroquinolone susceptibility in all Bangladeshi S. Paratyphi A isolates. Notably, we identified the pHCM2- like cryptic plasmid which was highly similar to S. Typhi plasmids circulating in Bangladesh and has not been previously identified in S. Paratyphi A organisms., Significance: This study demonstrates the utility of WGS to monitor the ongoing evolution of this emerging enteric pathogen. Novel insights into the genetic structure of S. Paratyphi A will aid the understanding of both regional and global circulation patterns of this emerging pathogen and provide a framework for future genomic surveillance studies., Competing Interests: The authors have declared that no competing interests exist.

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 I 2 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.

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., Competing Interests: The authors have declared that no competing interests exist.

Introduction: Typhoid fever (TF) continues to cause considerable morbidity and mortality in Nepal, but only limited epidemiologic data is available about TF outside Kathmandu., Methods: As part of an interventional trial, we performed a prospective cohort study of bacteremic TF patients in Dhulikhel Hospital between October 2012 and October 2014. Demographic, epidemiological, clinical, and microbiologic data were recorded., Results: 116 bacteremic typhoid patients were included in the study. Most were young, healthy, adults (mean age 27.9±12 years), 41.4% of whom were female. More than 70% of patients were employed in non-manual services or were university students. Salmonella Typhi accounted for 64/115 (55.7%) of all isolates, while Salmonella Paratyphi accounted for 51/115 (44.3%), of which 42 were Paratyphi A and 9 Paratyphi B. A significant proportion of TF cases occurred also during the dry season (48/116, 41.6%). The clinical presentation of Salmonella Typhi and Paratyphi infections was similar, except for a greater proportion of arthralgia in patients with Salmonella Typhi. Most Salmonella Typhi and Paratyphi isolates were resistant to nalidixic acid and susceptible to older antibiotics. One Salmonella Paratyphi isolate was resistant to ceftriaxone., Conclusions: TF remains common in the Dhulikhel area, even among those with a high level of education. Public health measures aimed at reducing the incidence of TF in the Dhulikhel area are warranted. The relative burden of TF caused by Salmonella Paratyphi is rising; a vaccine with activity against Salmonella Paratyphi is needed. Since Salmonella Paratyphi B was more prevalent in this cohort than in large cohorts of patients from Kathmandu, it is likely that there are significant regional variations in the epidemiology of TF outside Kathmandu., Competing Interests: The authors have declared that no competing interests exist.

Objective: To retrospectively analyze the antimicrobial resistance phenotype and molecular typing characteristics of Salmonella ( S .) typhi and S . paratyphi in Jiangsu province from 2012 to 2015. Methods: The samples were collected from typhoid and paratyphoid patients in Jiangsu province. The biochemical identification and serotyping were carried out after isolation and culture. Kirby-Bauer (K-B) testing was used to detect the drug susceptibility of the strains. The molecular typing characteristics of S . typhi and S . paratyphi were analyzed by pulsed field gel electrophoresis (PFGE). Results: The resistant rates of 134 S. typhi and S. paratyphi A strains to nalidixic acid were highest (61.2% and 86.7%), while the resistant rates to remaining antibiotics were less than 15.0%. Most of S. typhi and S. paratyphi A strains were resistant to only one antibiotic. Multidrug-resistant (MDR) strains of S. typhi and S. paratyphi A accounted for 2.6% and 13.3% respectively. The composition of the all-sensitive strains of S. typhi increased by 44.3% in 2015, at the same time, there were also MDR S. paratyphi A strains, which were resistant to 5 and 6 antibiotics. S. paratyphi A could be divided into eight molecular patterns by PFGE, showing that the similarity between the MDR strains and other strains was relatively low. The S. paratyphi A strains with same pattern were resistant to same antibiotics. S. typhi could be divided into 68 molecular patterns by PFGE, with large variability between different patterns. There was no corresponding relationship between the patterns and the drug resistance characteristics. Conclusions: The overall antibiotic resistance of S. typhi and S. paratyphi A strains showed a decreasing trend, but the number of antibiotics to which they were resistant increased. PFGE patterns of S. typhi showed diversity without correspondence to antibiotic characteristics. PFGE patterns of S. paratyphi A were less with correspondence to antibiotic characteristics. We should pay more attention to key patterns in key areas.

Background: Enteric fever remains a major public health problem in low resource settings and antibiotic resistance is increasing. In Asia, an increasing proportion of infections is caused by Salmonella enterica serovar Paratyphi A, which for a long time was assumed to cause a milder clinical syndrome compared to Salmonella enterica serovar Typhi., Methodology: A retrospective chart review study was conducted of 254 unique cases of blood culture confirmed enteric fever who presented at a referral adult hospital in Phnom Penh, Cambodia between 2008 and 2015. Demographic, clinical and laboratory data were collected from clinical charts and antibiotic susceptibility testing was performed. Whole genome sequence analysis was performed on a subset of 121 isolates., Results: One-hundred-and-ninety unique patients were diagnosed with Salmonella Paratyphi A and 64 with Salmonella Typhi. In the period 2008-2012, Salmonella Paratyphi A comprised 25.5% of 47 enteric fever cases compared to 86.0% of 207 cases during 2013-2015. Presenting symptoms were identical for both serovars but higher median leukocyte counts (6.8 x 109/L vs. 6.3 x 109/L; p = 0.035) and C-reactive protein (CRP) values (47.0 mg/L vs. 36 mg/L; p = 0.034) were observed for Salmonella Typhi infections. All but one of the Salmonella Typhi isolates belonged to haplotype H58 associated with multidrug resistance (MDR) (i.e. resistance to ampicillin, chloramphenicol and co-trimoxazole).;42.9% actually displayed MDR compared to none of the Salmonella Paratyphi A isolates. Decreased ciprofloxacin susceptibility (DCS) was observed in 96.9% (62/64) of Salmonella Typhi isolates versus 11.5% (21/183) of Salmonella Paratyphi A isolates (all but one from 2015). All isolates were susceptible to azithromycin and ceftriaxone., Conclusions: In Phnom Penh, Cambodia, Salmonella Paratyphi A now causes the majority of enteric fever cases and decreased susceptibility against ciprofloxacin is increasing. Overall, Salmonella Typhi was significantly more associated with MDR and DCS compared to Salmonella Paratyphi A.

To explore transmission patterns and genetic relationships of Salmonella enterica serovar Paratyphi A in China, we conducted a genome-wide single-nucleotide polymorphism analysis on the strains in the 4 provinces in which incidence was highest during 1998-2012. Markedly phylogeographic clustering suggested regional virus circulation after introduction from areas in southeastern China.

Objective: Establishment and application of Taq Man probe-based quadruple real-time PCR for detection of Salmonella paratyphi A/B/C and Salmonella typhi. Primers specific to Salmonella paratyphi A( SPAP), Salmonella paratyphi B( SPBP), Salmonella paratyphi C( SPCP), and Salmonella typhi( STP) were designed., Methods: A method of Taq Man probe-based quadruple real-time PCR was established according to the distinction of the 5'end of the probe mark of TET, ROX, FAM and HEX. 5 strains of SPA, 4 strains of SPB, 7 strains of SPC and 11 strains of ST were identified by amplification from SPAP, SPBP, SPCP and STP., Results: While other serotypes of salmonella and17 strains of non-salmonella got negative results of amplification. Amplification rate of SPAP, SPBP, SPCP, and STP were 84. 5%, 101. 8%, 92. 4% and 90. 9%, respectively. The linear correlation coefficient( R~2) were 0. 996, 0. 975, 0. 996 and 0. 984, respectively., Conclusion: The PCR system is specific and sensitive for the identification of SPA, SPB, SPC and ST.

In 2013, an unusual increase in the number of Salmonella enterica serotype Paratyphi A ( Salmonella Paratyphi A) infections was reported in patients in Phnom Penh, Cambodia, and in European, American and Japanese travellers returning from Cambodia. Epidemiological investigations did not identify a common source of exposure. To analyse the population structure and genetic diversity of these Salmonella Paratyphi A isolates, we used whole-genome sequencing on 65 isolates collected from 1999 to 2014: 55 from infections acquired in Cambodia and 10 from infections acquired in other countries in Asia, Africa and Europe. Short-read sequences from 80 published genomes from around the world and from 13 published genomes associated with an outbreak in China were also included. Pulsed-field gel electrophoresis (PFGE) was performed on a subset of isolates. Genomic analyses were found to provide much more accurate information for tracking the individual strains than PFGE. All but 2 of the 36 isolates acquired in Cambodia during 2013-2014 belonged to the same clade, C5, of lineage C. This clade has been isolated in Cambodia since at least 1999. The Chinese outbreak isolates belonged to a different clade (C4) and were resistant to nalidixic acid, whereas the Cambodian outbreak isolates displayed pan-susceptibility to antibiotics. Since 2014, the total number of cases has decreased, but there has been an increase in the frequency with which nalidixic acid-resistant C5 isolates are isolated. The frequency of these isolates should be monitored over time, because they display decreased susceptibility to ciprofloxacin, the first-choice antibiotic for treating paratyphoid fever.

Enteric fever is an invasive infection predominantly caused by Salmonella enterica serovars Typhi and Paratyphi A. The pathogens have evolved from other nontyphoidal salmonellaeto become invasive and host restricted. Emergence of antimicrobial resistance in typhoidal salmonellae in some countries is a major therapeutic concern as the travelers returning from endemic countries carry resistant strains to non endemic areas. In order to understand the epidemiology and to design disease control strategies molecular typing of the pathogen is very important. We performed Multilocus Sequence Typing (MLST) of 251 S. Typhi and 18 S. Paratyphi strains isolated from enteric fever patients from seven centers across India during 2010-2013to determine the population structure and prevalence of MLST sequence types in India. MLST analysis revealed the presence of five sequence types (STs) of typhoidal salmonellae in India namely ST1, ST2 and ST3 for S. Typhi and ST85 and ST129 for S. Paratyphi A.S. Typhi strains showed monophyletic lineage and clustered in to 3 Sequence Types-ST1, ST2 and ST3 and S. Paratyphi A isolates segregated in two sequence types ST85 and ST129 respectively. No association was found between antimicrobial susceptibility and sequence types. This study found ST1 as the most prevalent sequence type of S. Typhi in India followed by ST2, which is in concordance with previous studies and MLST database. In addition a rare sequence type ST3 has been found which is reported for the first time from the Indian subcontinent. Amongst S. Paratyphi A, the most common sequence type is ST129 as also reported from other parts of world. This distribution and prevalence suggest the common spread of the sequence types across the globe and these findings can help in understanding the disease distribution., Competing Interests: The authors have declared that no competing interests exist.

Background: Typhoid fever is classically caused by Salmonella enterica serotype typhi.Recently the frequency of isolation of S. paratyphi A (SPA) has been increased in comparison to S. typhi in Indian scenario., Aim: To observe the rate of isolation and antimicrobial susceptibility pattern of SPA from suspected enteric fever cases attending tertiary care centres of Eastern Orissa., Settings and Design: Retrospective study Materials and Methods: 1488 blood samples were collected during different duration of fever and cultured in BACTEC blood culture system and bottles showing signal for growth were subcultured and identified as Salmonella spp. by standard procedure and mini API (Biomeriux) and antimicrobial susceptibility by disc diffusion method., Statistical Analysis: Chi square test., Results: 167 Salmonella spp. were isolated including 83.8% Salmonella paratyphi A and 16.6% S. typhi. Among them 102 were males and 65 were females with mean age of 22.7 yrs. S. paratyphi A was the predominant spp. each year but during 2008 - 2011, there was a dramatic rise (significant P value- 0.034). Multidrug resistance was noticed in 10.2% of the isolates. 98% of S. paratyphi A were resistant to nalidixic acid and 41% to ciprofloxacin, but the MIC of ciprofloxacin was raised between 1-2 μgm/dl showing the relation between nalidixic acid resistance and raised MIC of ciprofloxacin., Conclusion: Nalidixic acid should be tested along with ciprofloxacin disc while testing for susceptibility and MIC of ciprofloxacin is mandatory before advocating therapy to prevent treatment failure.

In 2013, an unusual increase of paratyphoid fever cases in travellers returning from Cambodia was reported in Japan. From December 2012 to September 2013, 18 cases of Salmonella Paratyphi A infection were identified. Microbiological analyses revealed that most isolates had the same clonal identity, although the epidemiological link between these cases remains unclear. It was inferred that the outbreak was caused by a common and persistent source in Cambodia that was likely to have continued during 2014. The information of surveillance and laboratory data from cases arising in travellers from countries with limited surveillance systems should be timely shared with the country of origin.

Objective: To investigate the antibiotic resistance and pulsed field gel electrophoresis (PFGE) patterns of clinical isolates of Salmonella (S.) typhi and S. paratyphi in Henan province during 2009-2011., Methods: According to molecular typing and Salmonella K-B drug susceptibility test method published by international PulseNet bacterial infectious disease monitoring network and USA Clinical and Laboratory Standards Institute (CLSI), the drug susceptibility and PFGE molecule characteristics of 78 S. typhi and S. paratyphi strains isolated from sentinel hospitals in Henan were analyzed., Results: The 78 strains of S. typhi and S. paratyphi were resistant to 13 kinds of antibiotics, in which 62 were multidrug resistant (79.5%), 4 were resistant to 2-3 kinds of antibiotics (5.1%), 41 were resistant to 5-8 kinds of antibiotics (52.6%), 14 were resistant to 9-10 kinds of antibiotics (17.9%), 3 were resistant to 11-12 kinds of antibiotics (3.8%). The resistant rate to cephalosporins, quinolones and other 3 kinds of antibiotic showed an increase trends. Seventy two strains of S. typhi and S. paratyphi could be divided 14 molecular patterns by digestion with XbaⅠ and PFGE, each pattern contains 1-47 strains which shared the similarity of 66.03%-100.00%., Conclusions: The drug resistance of clinical isolates of S. typhi and S. paratyphi was serious in Henan. The PFGE patterns showed diversity, but the predominant patterns could be still found. The PFGE patterns of some strains were associated with their drug resistance.

Previously, the prevalence of Salmonella enterica Paratyphi A in Yunnan was high; and recently Yunnan was the predominant endemic province in China. To identify the molecular epidemiology, antibiotic resistance profile and genotypic diversity of the S. Paratyphi A isolates from 1995 to 2013 in Yunnan, we performed the study. Antibiotic susceptibility tests, pulse-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to identify the characteristics of the bacterial isolates. The results showed from 1995 to 2013, 366 S. Paratyphi A were isolated: 295 isolates (80.6%) from Yuxi and 68 isolates (18.58%) from Honghe. All of the strains were resistant to nalidixic acid, and some were resistant to ampicillin and trimethoprim/sulfamethoxazole in different years. All the isolates were sensitive to cefotaxime and ciprofloxacin. Identical PFGE with two enzyme digestion patterns were found for 339 isolates. Some environmental isolates in different years were homologous with the strains isolated from food and patients. MLST showed 349 strains were ST85, only 17 isolates were ST129. S. Paratyphi A isolates from Yunnan showed a high similarity, and we found the pathogen isolated from patients, the environment and food had the close epidemiological relationship, forming a transmission circulation. These findings have important implications for paratyphoid-control strategies., (Copyright © 2014 Elsevier B.V. All rights reserved.)

The objective of the study was to conduct bacteriological analysis of water with special reference to Salmonella spp from natural sources of rural habitations of East Sikkim. A total of 28 Salmonella serovars isolated were biotyped, phage typed and tested for their anti-microbial susceptibility. All the isolates of Salmonella enterica serovar Typhi belonged to Biotype I. Four isolates of S. typhi belonged to phage type A. All S. paratyphi A isolates belong to phage 2. All the isolates were sensitive to chloramphenicol, cefixime and amikacin. Untreated natural water sources are unsafe for human consumption.

The aim of the present study was to genotype Salmonella enterica serotype paratyphi A (SPA) isolated from Yuxi, China, in a multiple-locus variable number of tandem repeats (VNTRs) analysis (MLVA) and to compare them with isolates from the Chinese Medical Culture Collection Center (CMCC). Potential VNTRs were screened from the genomes of ATCC9150 and AKU_12601 using the Tandem Repeats Finder program. Nine VNTRs were established for MLVA typing of 195 SPA isolates from Yuxi and 20 isolates from CMCC. The dendogram for MLVA profiles and minimum spanning tree (MST) were drawn using the categorical coefficient calculated by BioNumerics software. A total of 23 MLVA types were identified in 215 SPA isolates and were grouped into six distinct cluster groups A, B, C, D, E and F. A total of 195 Yuxi SPA isolates were exclusively grouped into cluster C with nine MLVA genotypes. A total of 20 CMCC isolates were grouped in clusters A B, D, E and F with the other 14 MLVA types. The MLVA with nine VNTR loci, which was exploited in the present study, represents a successful strategy for genotyping SPA. Furthermore, the 195 Yuxi isolates appear to be closely related to each other and distinct from the 20 CMCC strains.

Background: In Asia, Salmonella Paratyphi A is an emerging infection, and travelers are increasingly at risk. During October 2009-November 2009, an outbreak in S. Paratyphi A infection was noted in Israeli travelers returning from Nepal., Methods: An outbreak investigation included a standardized exposure questionnaire admitted to all patients and medical chart abstraction. Isolates were tested for antimicrobial susceptibility and pulsed-field gel electrophoresis (PFGE)., Results: During 1 October 2009-30 November 2009, 37 Israeli travelers returning from Nepal were diagnosed with S. Paratyphi A bacteremia. All 37 case isolates had an identical pattern on PFGE, and all were nalidixic acid resistant. Only 1 food venue was frequented by all the outbreak cases, with the largest number of exposures occurring around the Jewish New Year. All patients recovered without complications. Time to defervescence in 17 patients treated with ceftriaxone and azithromycin combination was 3.2 days (± 1.7), whereas in 13 cases treated with ceftriaxone monotherapy, the time to defervescence was 6.6 days (± 1.8; P < .001)., Conclusions: A point-source, "Paratyphoid Mary"-like outbreak was identified among Israeli travelers to Nepal. Combination Ceftriaxone-Azithromycin therapy may provide a therapeutic advantage over monotherapy, and merits further clinical trials.

Salmonella enterica serovar Paratyphi A infection has caused public health problems in some countries in recent years. Pulsed-field gel electrophoresis (PFGE) has been used for the subtyping and epidemiological investigations of some serotypes of Salmonella, mainly in outbreaks caused by non-typhoidal Salmonella. In this study, different restriction endonucleases and electrophoresis parameters were compared for the PFGE subtyping by using Salmonella Paratyphi A strain panels. Two protocols for the enzymes SpeI and XbaI showed higher discriminatory power, which may facilitate epidemiological analysis for more accurate case definition, and clonality study of Salmonella Paratyphi A.

Typhoid is a systemic infection caused by Salmonella Typhi and Salmonella Paratyphi A, human-restricted bacteria that are transmitted faeco-orally. Salmonella Typhi and S. Paratyphi A are clonal, and their limited genetic diversity has precluded the identification of long-term transmission networks in areas with a high disease burden. To improve our understanding of typhoid transmission we have taken a novel approach, performing a longitudinal spatial case-control study for typhoid in Nepal, combining single-nucleotide polymorphism genotyping and case localization via global positioning. We show extensive clustering of typhoid occurring independent of population size and density. For the first time, we demonstrate an extensive range of genotypes existing within typhoid clusters, and even within individual households, including some resulting from clonal expansion. Furthermore, although the data provide evidence for direct human-to-human transmission, we demonstrate an overwhelming contribution of indirect transmission, potentially via contaminated water. Consistent with this, we detected S. Typhi and S. Paratyphi A in water supplies and found that typhoid was spatially associated with public water sources and low elevation. These findings have implications for typhoid-control strategies, and our innovative approach may be applied to other diseases caused by other monophyletic or emerging pathogens.

Objectives: To determine the minimum inhibitory concentrations (MICs) of ceftriaxone, azithromycin, pefloxacin, cefipime and imipenem for Salmonella Typhi (S. Typhi) and Paratyphi., Methods: One hundred and fifty four isolates of Salmonella Typhi and S. Paratyphi A, B and C growing in blood culture were selected. MICs of ceftriaxone, azithromycin, pefloxacin, cefipime and imipenem were performed by agar dilution method as recommended by clinical laboratory standard institutes., Results: MIC90 of azithromycin and pefloxacin was 8 microg/ml, cefipime was 0.06 microg/ml and imipenem was 0.5 microg/ml. None of the strains were found to be resistant to ceftriaxone but 3 isolates showed higher MIC value of 2 microg/ml., Conclusion: Azithromycin appears a suitable alternate for the treatment of typhoid in the community. Imipenem and cefipime are good options in complicated cases to be treated in hospital settings. Pefloxacin cannot be used as MICs are higher. Presence of isolates with higher MIC of ceftriaxone is serious and stresses upon continuous laboratory surveillance to guide clinicians appropriately.

Salmonella enterica serotype Paratyphi A is a highly clonal organism; pulsed-field gel electrophoresis (PFGE) is insufficient in discriminating isolates. A multilocus variable-number tandem repeat analysis (MLVA) was developed, and its usefulness in discriminating isolates was compared. PFGE analysis with XbaI and BlnI discriminated 55 isolates into 14 types, with a discriminatory index (DI) of 0.741 (confidence interval [CI], 0.635-0.847). MLVA divided the isolates into 23 types, with a DI of 0.937 (CI, 0.909-0.964), which was significantly higher than that for PFGE. Clustering analysis of PFGE and MLVA patterns indicated that S. Paratyphi A isolates recovered from 2000 to 2010 in South and Southeast Asia were highly clonal. Although MLVA is not sufficiently powerful in discriminating epidemiologically unrelated isolates, it can complement PFGE for epidemiologic investigation of S. Paratyphi A infections., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Objective: To analyze molecular and evolution characteristics of Salmonella Paratyphi A isolates from 2000 to 2008, China., Methods: Using pulsed-field gel electrophoresis (PFGE) method with SpeI restriction enzyme, and multilocus sequence typing (MLST) method based on housekeeping genes (aroC, thrA, hisD, purE, sucA, dnaN, hemD, adk, and purA), the genomic variations of 118 Salmonella Paratyphi A isolates from 10 regions during 2000 to 2008 were analyzed., Results: Using PFGE method, 118 Salmonella Paratyphi A isolates were clustered into 32 PFGE patterns, and 5 patterns were predominant (5 isolates or above). However, only 2 MLST types were identified for all isolates with MLST method. Among all Salmonella Paratyphi A isolates, the sequences of housekeeping genes were highly conservative and showed a high degree of cloning., Conclusion: For Chinese epidemic Salmonella Paratyphi A isolates during 2000 - 2008, MLST method showed low discrimination power and the MLST method should not be applied to outbreak and epidemiological surveillance of Salmonella Paratyphi A. Currently, nationwide paratyphoid fever epidemics is caused by highly clonal isolates in China. As the time changes, these isolates also accumulate sporadic mutations.

In this study, we developed a multiplex polymerase chain reaction (mPCR) assay for pan-Salmonella detection as well as for specific detection of serovars Typhi and Paratyphi A. The assay detects members of the Salmonella genus by amplifying the outer membrane protein C (ompC). The presence of either Salmonella serovar Typhi or Paratyphi A is indicated by amplification of the putative regulatory protein gene STY4220, which is common to both serovars. Further differentiation of the serovars was achieved by targeting the intergenic region (SSPAI) between SSPA1723a and SSPA1724 in serovar Paratyphi A, and stgA, a fimbrial subunit protein, in serovar Typhi. mPCR was evaluated using 124 clinical and reference Salmonella serovars. S. enterica serovars Typhi and Paratyphi A were detected at 100% specificity and sensitivity. Each PCR reaction detected approximately 1 pg of Salmonella genomic DNA. Sensitivity of the PCR when tested on 8-h-enriched spiked blood samples of serovars Typhi and Paratyphi A was estimated at 4.5 x 10(4)-5.5 x 10(4)CFU/ml, with similar detection levels observed for spiked fecal samples. This mPCR could prove to be a useful diagnostic tool for the detection and differentiation of serovars Typhi and Paratyphi A., ((c) 2010 Elsevier Masson SAS. All rights reserved.)

Typhoid fever is becoming an ever increasing threat in the developing countries. We have improved considerably upon the existing PCR-based diagnosis method by designing primers against a region that is unique to Salmonella enterica subsp. enterica serovar Typhi and Salmonella enterica subsp. enterica serovar Paratyphi A, corresponding to the STY0312 gene in S. Typhi and its homolog SPA2476 in S. Paratyphi A. An additional set of primers amplify another region in S. Typhi CT18 and S. Typhi Ty2 corresponding to the region between genes STY0313 to STY0316 but which is absent in S. Paratyphi A. The possibility of a false-negative result arising due to mutation in hypervariable genes has been reduced by targeting a gene unique to typhoidal Salmonella serovars as a diagnostic marker. The amplified region has been tested for genomic stability by amplifying the region from clinical isolates of patients from various geographical locations in India, thereby showing that this region is potentially stable. These set of primers can also differentiate between S. Typhi CT18, S. Typhi Ty2, and S. Paratyphi A, which have stable deletions in this specific locus. The PCR assay designed in this study has a sensitivity of 95% compared to the Widal test which has a sensitivity of only 63%. As observed, in certain cases, the PCR assay was more sensitive than the blood culture test was, as the PCR-based detection could also detect dead bacteria.

We described a 5-min colorimetric test for paratyphoid A fever, which detects anti-Salmonella O2 antibodies by inhibiting the binding between 2 types of reagent particles. This test (TUBEX-PA) is based on that (TUBEX-TF) used for typhoid fever, which detects anti-O9 antibodies. TUBEX-PA showed a sensitivity of 81.0% (47/58 culture-confirmed patients) to 93.3% (14/15) and was 98.1% (52/53) specific for healthy subjects. However, TUBEX-PA also detected 50% (7/14) to 81.8% (9/11) of typhoid patients, and conversely, TUBEX-TF detected 46.7% (7/15) to 73.3% (11/15) of paratyphoid A cases. This cross-detection could be abrogated in both tests by adding a blocker (heterologous antigen) to remove the antibodies responsible, which presumably bind to a common antigen (O12) located close to O2 and O9. The presence of anti-O12 antibodies in typhoid (9/12 or 75.0% sensitive) and paratyphoid A (22/33 or 66.7%) patients was demonstrated directly using a prototypic TUBEX test designed specifically to detect these antibodies. Thus, using TUBEX-PA and TUBEX-TF together can increase the diagnostic accuracy of detecting both typhoid and paratyphoid A fever, while the further use of differential tests allows possible immediate discrimination between these diseases.

Salmonella enterica serovar Paratyphi A is a causative agent of paratyphoid fever. The clinical syndrome caused by paratyphoid fever overlaps with other febrile illnesses and cannot be distinguished from typhoid fever. Conventional methods used for diagnosis are time consuming, costly, and labor-intensive. We evaluated the specificity, sensitivity, and application of a multiplex polymerase chain reaction (PCR) previously developed by the method (Ou, H.Y., Teh, C.S.J., Thong, K.L., et al., J. Mol. Diagn., 9, 624-630, 2007) using 6 S. Paratyphi A, 22 S. Typhi, and 85 other Salmonella serovars as well as 36 non-Salmonella strains. The detection limit of the multiplex PCR was 4 x 10(4) cfu ml(-1). In a blind test of the other 50 strains, this multiplex PCR correctly identified the only S. Paratyphi A in the panel of strains. The sensitivity of this PCR using spiked blood and stool samples was 1 x 10(5) cfu ml(-1) and 2 x 10(5) cfu ml(-1), respectively, but increased to 1 x 10(4) cfu ml(-1) and 2 x 10(3) cfu ml(-1) after 5-h enrichment. We believe that this multiplex PCR is a promising technique for the specific and sensitive detection of S. Paratyphi A in clinical, environmental, and food samples.

Between January 2005 and December 2006, a higher incidence of paratyphoid fever (53.8%) compared to typhoid fever (44.9%) has been observed at a tertiary hospital in South India. A definite seasonal pattern of incidence is seen in paratyphoid fever (peak incidence during October-December, i.e., post monsoon period) but not in typhoid fever. Decreased fluoroquinolone susceptibility is much higher in S. Paratyphi A (98.8%) as compared to S. Typhi (46.5%). These findings are of importance in therapeutic decision making, development of vaccination strategies and implementing public health measures for disease control.

Objective: To analyze the molecular types of Salmonella paratyphi A strains isolated in the recent years, and to construct the standard S. paratyphi A databank in the laboratory surveillance network PulseNet China., Methods: S. paratyphi A isolates from 4 provinces were analyzed with the standard pulsed-field gel electrophoresis (PFGE) protocol used in PulseNet and their patterns compared. The databank was constructed with BioNumerics., Results: Eleven PFGE patterns were obtained, in which 3 predominant patterns were identifies with a similarity coefficient of 96.3%. The strains of these patterns, accounted for 86.5% of the analyzed strains, appeared in different provinces and years., Conclusion: The databank of S. paratyphi A was constructed and could be used in laboratory surveillance of S. paratyphi A in PulseNet China. From the analyses on molecular typing of the isolates, data suggested that the predominant strains might cause the epidemics in different regions.

Salmonella enterica serovars Typhi, Paratyphi A, and Sendai are human-adapted pathogens that cause typhoid (enteric) fever. The acute prevalence in some global regions and the disease severity of typhoidal Salmonella have necessitated the development of rapid and specific detection tests. Most of the methodologies currently used to detect serovar Typhi do not identify serovars Paratyphi A or Sendai. To assist in this aim, comparative sequence analyses were performed at the loci of core bacterial genetic determinants and Salmonella pathogenicity island 2 genes encoded by clinically significant S. enterica serovars. Genetic polymorphisms specific for serovar Typhi (at trpS), as well as polymorphisms unique to human-adapted typhoidal serovars (at sseC and sseF), were observed. Furthermore, entire coding sequences unique to human-adapted typhoidal Salmonella strains (i.e., serovar-specific genetic loci rather than polymorphisms) were observed in publicly available comparative genomic DNA microarray data sets. These polymorphisms and loci were developed into real-time PCR, standard PCR, and liquid microsphere suspension array-based molecular protocols and tested for with a panel of clinical and reference subspecies I S. enterica strains. A proportion of the nontyphoidal Salmonella strains hybridized with the allele-specific oligonucleotide probes for sseC and sseF; but the trpS allele was unique to serovar Typhi (with a singular serovar Paratyphi B strain as an exception), and the coding sequences STY4220 and STY4221 were unique among serovars Typhi, Paratyphi A, and Sendai. These determinants provided phylogenetic data on the genetic relatedness of serovars Typhi, Paratyphi A, and Sendai; and the protocols developed might allow the rapid identification of these Salmonella serovars that cause enteric fever.

Background: Enteric fever is a major global problem. Emergence of antibacterial resistance threatens to render current treatments ineffective. There is little research or public health effort directed toward Salmonella enterica serovar Paratyphi A, because it is assumed to cause less severe enteric fever than does S. enterica serovar Typhi. There are few data on which to base this assumption, little is known of the serovar's antibacterial susceptibilities, and there is no readily available tolerable vaccination., Methods: A prospective study was conducted of 609 consecutive cases of enteric fever (confirmed by blood culture) to compare the clinical phenotypes and antibacterial susceptibilities in S. Typhi and S. Paratyphi A infections. Variables independently associated with either infection were identified to develop a diagnostic rule to distinguish the infections. All isolates were tested for susceptibility to antibacterials., Results: Six hundred nine patients (409 with S. Typhi infection and 200 with S. Paratyphi A infection) presented during the study period. The infections were clinically indistinguishable and had equal severity. Nalidixic acid resistance, which predicts a poor response to fluoroquinolone treatment, was extremely common (75.25% of S. Paratyphi A isolates and 50.5% of S. Typhi isolates; P < .001). S. Paratyphi A was more likely to be resistant to ofloxacin (3.6% vs. 0.5%; P = .007) or to have intermediate susceptibility to ofloxacin (28.7% vs. 1.8%; P < .001) or ciprofloxacin (39.4% vs. 8.2%; P < .001). MICs for S. Paratyphi A were higher than for S. Typhi (MIC of ciprofloxacin, 0.75 vs. 0.38 microg/mL [P < .001]; MIC of ofloxacin, 2.0 vs. 0.75 microg/mL [P < .001])., Conclusions: The importance of S. Paratyphi A has been underestimated. Infection is common, the agent causes disease as severe as that caused by S. Typhi and is highly likely to be drug resistant. Drug resistance and lack of effective vaccination suggest that S. Paratyphi A infection may become a major world health problem.

The present study was undertaken to compare the changing trends of antibiograms of Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A isolates. A total of 80 isolates of salmonella obtained from blood cultures between 2001-2004 were included in the study. Identification and antibiotic sensitivities of the isolates were performed by using mini API (bio Merieux, France). Sixty isolates were identified as Salmonella enterica serovar Typhi and 20 were identified as Salmonella enterica serovar Paratyphi A. More than 67% of S.typhi and 80% of S.paratyphi A isolates were sensitive to chloramphenicol. Sensitivity of S.typhi isolates to cephalosporins was found to have increased from 2001-2004 while that of S.paratyphi A showed a decline. With increasing resistance to ciprofloxacin and the possibility of re-emergence of sensitivity to chloramphenicol, the policy of empirical treatment of enteric fever needs to be rationalized.

Mutations in gyrA in strains of Salmonella enterica serotypes Typhi and Paratyphi A have been characterised by a LightCycler-based PCR-hybridisation gyrA mutation assay (GAMA) and by DNA sequencing. Four mutations (Ser-83 to Phe, Asp-87 to Asn, Ser-83 to Tyr and Asp-87 to Gly) have been identified in 13 strains of Typhi and three strains of Paratyphi A resistant to nalidixic acid (=nal(r)) and with decreased susceptibility to ciprofloxacin (=Cp(L)), with the mutation Ser-83 to Phe predominating. The results have demonstrated heterogeneity in gyrA in nal(r) Cp(L) strains of Typhi and Paratyphi A and may be useful for epidemiological investigations. No mutations in gyrA were identified in four Cp(L) strains of S. Typhi that were sensitive to nalidixic acid. The mechanism of decreased susceptibility to ciprofloxacin in these strains is under investigation.

Multidrug resistance among Salmonella typhi is well known. Reports of treatment failure in enteric fever with Ciprofloxacin made us undertake this study to determine the antibiotic susceptibility pattern of S. typhi and S. paratyphi A isolated from typhoid bacteremia cases, by disc diffusion and MIC by broth dilution method. A total of 50 strains were tested, 48 of Salmonella typhi and 2 of S. paratyphi A. The disc diffusion method was done using ampicillin, chloramphenicol, cotrimoxazole, tetracycline, ciprofloxacin, ofloxacin, cefuroxime and ceftriaxone as antibiotics. The MIC was performed using ciproloxacin, ofloxacin and ceftriaxone based on standard procedure. ACCOT resistance as determined by disc diffusion method was seen in 68% of isolates. All the strains remained susceptible to flouroquinolones cephalosporins and aminoglycosides. The MIC of ciprofloxacin, ofloxacin and ceftriaxone were in the recommended range of susceptibility as given by NCCLS, 14 (28%) strains had MIC of ciprofloxacin greater than 0.5 ug/ml with 4 strains having an MIC of 1.56 ug/ml; 25 (50%) strains had MIC of ofloxacin greater than 0.5 ug/ml and 20 (40%) strains had MIC of ceftriaxone greater than 0.5 ug/ml. The high levels of MIC of ciprofloxacin may account for treatment failure cases. The rising levels of MIC of ofloxacin and ceftriaxone in S. typhi and S. paratyphi is also of concern. We document here the emergence of high levels of MIC not only to ciprofloxacin, but also ofloxacin and ceftriaxone in S. typhi and S. paratyphi A. We recommend that MIC levels of ofloxacin and ceftriaxone should be monitored along with ciprofloxacin in treatment failure cases of enteric fever.

The PCR primers for O, H, and Vi antigen genes, tyv (rfbE), prt (rfbS), fliC-d, fliC-a, and viaB, were designed and used for the rapid identification of Salmonella enterica serovars Typhi and Paratyphi A with multiplex PCR. The results showed that all the clinical isolates examined of Salmonella serovars Typhi and Paratyphi A were accurately identified by this assay.

Aims: Subtyping of Salmonella Paratyphi A isolates from India, Pakistan, Indonesia and Malaysia was carried out by pulsed-field gel electrophoresis (PFGE) to assess the extent of genetic diversity of these isolates from different endemic countries., Methods and Results: A total of 39 human isolates of Salmonella Paratyphi A from Pakistan, India, Indonesia and Malaysia were studied using PFGE analysis following digestion of chromosomal DNA with XbaI. Seven isolates from Pakistan were resistant to ampicillin, tetracycline and cotrimoxazole. It was noted that Salmonella Paratyphi A isolates obtained from outbreaks in India had limited genetic diversity and probably belonged to closely related clones. Significant genetic homogeneity was observed among antimicrobial-resistant isolates from Pakistan and antimicrobial-sensitive isolates from Pakistan and Indonesia, respectively., Conclusions: PFGE was a useful subtyping technique to differentiate Salmonella Paratyphi A from different endemic countries. However, it fails to differentiate the antimicrobial-resistant and -sensitive strains., Significance and Impact of the Study: The findings of the present study verify the usefulness of PFGE in characterizing and comparing strains of Salmonella Paratyphi A. Our study suggests that a limited number of clones are responsible for paratyphoid fever in these countries.

During the post monsoon season of 1996 an outbreak of human Salmonellosis caused by Salmonella serovar-paratyphi A occurred in New Delhi and had continued for over 2 months. A total of 36 clinically diagnosed enteric-fever cases were reported during this outbreak. The isolates were compared following their characterisation by biotyping, antibiogram-analysis, plasmid-profiling and IS200 probing, to study the relatedness in order to delineate a common source. The study included representative strains from both outbreak (15) and sporadic (7) cases for comparative analysis. Biotyping, antibiogram, whole cell protein-analysis and plasmid-profiling could not discriminate sporadic cases from outbreak strains, suggesting that a single clone/type (PT-1) may be prevalent in our region. In contrast, molecular-typing using IS200-probing revealed 2 clonally related strains circulating during the outbreak, as compared to the unrelated sporadic strains which exhibited considerable genetic diversity. Molecular analysis by IS200-probing, helped to assign an index case which provided a history of later outbreaks, since paratyphi A was repeatedly cultured in later outbreaks also. The study also suggests that genetic rearrangements can occur during the emergence of outbreaks. It reaffirmed the usefulness of IS200-probing in epidemiological investigations of Salmonella enterica serovars.

We propose Salmonella paratyphi sp. nov., nom. rev., by raising Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A to species status and request an Opinion to include the specific epithet paratyphi in the binary combination of Salmonella paratyphi in the list of epitheta specifica conservanda.

During the period from 1993 to 1996, a total of 27,497 Salmonella isolates from humans, chicken meat, ready-to-eat Thai foods and shrimps were serotyped to know the predominant serovars of Salmonella in humans and foods in Thailand. Seventy-two and 81 serovars of Salmonella were identified in human and food samples, respectively. The significance of foods as a vehicle for human salmonellosis was discussed from an epidemiological viewpoint.

Two hundred and fourteen isolates of Salmonella typhi submitted to our laboratory between 1992 and 1996 were tested for susceptibility to 20 antimicrobial agents. Forty-eight of the 214 isolates (22.4%), recovered from individuals who had travelled in South Asia, were multiresistant. Forty-four of the 48 isolates were resistant to ampicillin, chloramphenicol, tetracycline, streptomycin, sulfamethoxazole, trimethoprim, cotrimoxazole, ticarcillin, and piperacillin; the other four isolates were resistant to four to six agents. Forty-two of the multiresistant isolates belonged to Vi phage type E1, two isolates from the Punjab State belonged to phage type A, another from the Punjab State belonged to phage type E3, one isolate from Pakistan belonged to type M1, and one isolate from India belonged to type J1. Plasmids from 45 of 48 isolates showed a temperature-sensitive mechanism of transfer to Escherichia coli K-12 strains, characteristic of H1 incompatibility group plasmids. The majority of plasmids had an estimated molecular weight of 120 MDa and encoded both citrate utilization and mercury resistance. Plasmids from three isolates had an estimated molecular weight of 112-115 MDa; one of these isolates encoded citrate utilization but not mercury resistance. Analysis of isolates by pulsed-field gel electrophoresis after digestion with XbaI and SpeI indicated that the majority of multiresistant isolates shared a common restriction profile, while four isolates had unique patterns.

The results of the rapid method for the detection and identification of epidemically related and unrelated causative agents of Salmonella infections. To analyze the chromosomal DNA of these strains, rapid polymerase chain reaction (PCR) was used. The analysis of the electrophoregrams of products obtained in rapid PCR revealed that the number of DNA fragments is constant for the cultures of the concrete serovar or phagovar. Using rapid PCR, the detection of S. typhi atypical strains was succeeded.

Salmonella paratyphi B and Salmonella java are biovars of common serotype 1,4,[5],12:b:1,2 which respectively cause human paratyphoid fever and gastroenteritis. In order to define genotypes and phylogenetic relationships in this group, we examined representative strains for restriction fragment length polymorphisms (RFLPs) in and around the 16S ribosomal RNA (rrn) genes, and the five to eleven insertion sites of the Salmonella-specific DNA insertion sequence IS200. One of four 16S rrn profiles was predominant, and was shared by the majority of strains, irrespective of their designation as S. paratyphi B or S. java. On the other hand, thirteen unique IS200 profiles were found and this technique was able to distinguish, for the first time, distinct genotypes for S. paratyphi B and S. java. One of the S. paratyphi B profiles, Spj-IP1.0, represented a globally-distributed clone. Greater diversity was detected within IS200 profiles of S. java than within those of S. paratyphi B. IS200 profiles described a phylogenetic complex in which strains of both biovars could be placed. They constituted reproducible molecular fingerprints, which could be compared in a band-matching database suitable for molecular epidemiological typing.

Genetic diversity and relationships among 123 strains of Salmonella paratyphi B (serotype 1,4,[5],12:b:[1,2]) were estimated from an assessment of electrophoretically demonstrable allelic variation at 24 chromosomal enzyme gene loci. Fourteen electrophoretic types, marking clones, were distinguished, the phylogeny of the clonal lineages was reconstructed, and biotype and other phenotypic characters were mapped onto this structure. Most d-tartrate-negative strains are members of an abundant, globally distributed clone (Pb 1) that is polymorphic for many biotype characters (including d-tartrate utilization), bacteriophage type, rRNA pattern, and colicin M and phage ES18 sensitivity. This clone is largely responsible for S. paratyphi B enteric fever in humans. In contrast, d-tartrate-positive strains (formerly known as S. java) occurred in all seven of the clonal lineages identified by population genetic analysis, although most d-tartrate-positive isolates belong to only two clones (Pb 3 and Pb 4), which vary in frequency geographically. Monophasic strains represent four closely related clones forming a distinctive phylogenetic lineage. The Kauffmann hypothesis of convergence in serotype among distantly related cell lineages through recombination (via phage transduction or other means) may account for the considerable genotypic diversity among clones of S. paratyphi B. Pb 4, Pb 6, and Pb 7 are more closely allied with clones of S. typhimurium and S. saintpaul than with other clones of S. paratyphi B. Sensitivity or resistance to colicin M and phage ES18 and the electrophoretic pattern of the rRNA, which were incorporated into a recently proposed scheme for the identification of types of S. paratyphi B, individually or in combination fail to mark clones or other meaningful phylogenetic subdivisions.