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We describe here the draft genome sequence and basic characteristics of Escherichia coli isolate INF13/18/A, which was isolated from Universiti Sains Malaysia (USM) Hospital. This isolate was identified as an extended-spectrum β-lactamase-producing Escherichia coli strain harboring the antimicrobial resistance genes TEM, CTX-M-1, and CTX-M-9.

This study is a cross-sectional, observational analysis of the COVID-19 pandemic in Africa, to understand the progression of the disease across the continent. Published data on COVID-19 from 20 January 2020 to 21 June 2021 were obtained and analyzed. Case fatality ratios, as well as case growth rates and other indices were computed. On 21 June 2021, a total of 178,210,532 confirmed cases and 3,865,978 deaths had been recorded worldwide. While the Americas recorded the highest number of cases, Southern Africa recorded the majority of African cases. Fatality rate since from 20 February 2020 to 21 June 2021 was highest in the Americas (2.63%) and low in the South Eastern Asia region (1.39%), globally increasing from 2.17% at the end of January to 6.36% in May 2020 and decreasing to a range between 2.14% to 2.30% since January 2021. In Africa, the infection rate per 100,000 persons was up to 3090.18, while deaths per 100,000 and case fatality ratio were as high as 119.64 and 5.72%, respectively, among the 20 most-affected countries. The testing rate per million population was highest in Botswana (512,547.08). Fatality appears to be increasing in some regions of Africa. The rate of infection and fatality in Africa could still likely take an upward turn. Strict control measures are required, considering the continent’s weak healthcare systems.

Typhoid fever, also known as typhoid, is a life-threatening bacterial infection that remains a global health concern. The infection is associated with a significant morbidity and mortality rate, resulting in an urgent need for specific and rapid detection tests to aid prevention and management of the disease. The present review aims to assess the specificity and sensitivity of the available literature on the immunodiagnostics of typhoid fever. A literature search was conducted using three databases (PubMed, ProQuest and Scopus) and manual searches through the references of identified full texts to retrieve relevant literature published between 1 January 2011 and 31 December 2020. Of the 577 studies identified in our search, 12 were included in further analysis. Lipopolysaccharides (LPS) and hemolysin E (HlyE) were the most frequently studied antigens. The specimens examined in these studies included serum and saliva. Using blood culture as the gold standard, anti-LPS IgA gave the highest sensitivity of 96% (95% CI: 93–99) and specificity of 96% (95% CI: 93–99) for distinguishing between typhoid cases and healthy controls, whereas the combination of anti-LPS and anti-flagellin total IgGAM gave the highest sensitivity of 93% (95% CI: 86–99) and specificity of 95% (95% CI: 89–100) for distinguishing typhoid cases and other febrile infections. A comparably high sensitivity of 92% (95% CI: 86–98) and specificity of 89% (95% CI: 78–100) were shown in testing based on detection of the combination of anti-LPS (IgA and IgM) and anti-HlyE IgG as well as a slightly lower sensitivity of 91% (95% CI: 74–100) in the case of anti-50kDa IgA. Anti-50kDa IgM had the lowest sensitivity of 36% (95% CI: 6–65) against both healthy and febrile controls. The development of a rapid diagnostic test targeting antibodies against lipopolysaccharides combined with flagellin appeared to be a suitable approach for the rapid detection test of typhoid fever. Saliva is added benefit for rapid typhoid diagnosis since it is less invasive. As a result, further studies could be done to develop additional approaches for adopting such samples.

The Gram-negative pathogenic spirochetal bacteria Leptospira spp. cause leptospirosis in humans and livestock animals. Leptospira kmetyi strain LS 001/16 was isolated from a soil sample associated with a leptospirosis patient in Kelantan, which is among the states in Malaysia with a high reported number of disease cases. Here, we report the complete genome sequence of Leptospira kmetyi strain LS 001/16.

Melioidosis is a severe disease caused by Burkholderia pseudomallei (B. pseudomallei), a Gram-negative environmental bacterium. It is endemic in Southeast Asia and Northern Australia, but it is underreported in many other countries. The principal routes of entry for B. pseudomallei are skin penetration, inhalation, and ingestion. It mainly affects immunocompromised populations, especially patients with type 2 diabetes mellitus. The laboratory diagnosis of melioidosis is challenging due to its non-specific clinical manifestations, which mimic other severe infections. The culture method is considered an imperfect gold standard for the diagnosis of melioidosis due to its low sensitivity. Antibody detection has low sensitivity and specificity due to the high seropositivity among healthy people in endemic regions. Antigen detection using various proteins has been tested for the rapid determination of B. pseudomallei; however, it presents certain limitations in terms of its sensitivity and specificity. Therefore, this review aims to frame the present knowledge of a potential target known as the Burkholderia invasion protein D (BipD), including future directions for its detection using an aptamer-based sensor (aptasensor).

The detection and measurement of different antibody isotypes in the serum provide valuable indicators of the different stages of typhoid infection. Here, the ability of S. Typhi recombinant hemolysin E (HlyE) to detect multi-isotype antibody responses in sera of patients with typhoid and paratyphoid A was investigated using an indirect antibody immunoassay. Nanogram amounts of HlyE were found to be sufficient for detection of IgG and IgA isotypes and, in a study of individuals' sera (n = 100), the immunoassay was able to distinguish between typhoid and non-typhoid sera. The overall sensitivity, specificity and efficiency of the ELISA were 70% (39/56), 100% (44/44) and 83% respectively.

Background Since 2000, the widespread adoption of pneumococcal conjugate vaccines (PCVs) has had a major impact in the prevention of pneumonia. Limited access to international financial support means some middle-income countries (MICs) are trailing in the widespread use of PCVs. We review the status of PCV implementation, and discuss any needs and gaps related to low levels of PCV implementation in MICs, with analysis of possible solutions to strengthen the PCV implementation process in MICs. Main body We searched PubMed, PubMed Central, Ovid MEDLINE, and SCOPUS databases using search terms related to pneumococcal immunization, governmental health policy or programmes, and MICs. Two authors independently reviewed the full text of the references, which were assessed for eligibility using pre-defined inclusion and exclusion criteria. The search terms identified 1,165 articles and the full texts of 21 were assessed for suitability, with eight articles included in the systematic review. MICs are implementing PCVs at a slower rate than donor-funded low-income countries and wealthier developed countries. A significant difference in the uptake of PCV in lower middle-income countries (LMICs) (71%) and upper middle-income countries (UMICs) (48%) is largely due to an unsuccessful process of “graduation” of MICs from GAVI assistance, an issue that arises as countries cross the income eligibility threshold and are no longer eligible to receive the same levels of financial assistance. A lack of country-specific data on disease burden, a lack of local expertise in economic evaluation, and the cost of PCV were identified as the leading causes of the slow uptake of PCVs in MICs. Potential solutions mentioned in the reviewed papers include the use of vaccine cost-effectiveness analysis and the provision of economic evidence to strengthen decision-making, the evaluation of the burden of disease, and post-introduction surveillance to monitor vaccine impact. Conclusion The global community needs to recognise the impediments to vaccine introduction into MICs. Improving PCV access could help decrease the incidence of pneumonia and reduce the selection pressure for pneumococcal antimicrobial resistance. Electronic supplementary material The online version of this article (doi:10.1186/s41479-017-0030-5) contains supplementary material, which is available to authorized users.

Please note that an author has been erroneously omitted from the author list of the published article [1].

Salmonella enterica subsp. enterica serovar Typhi is a human-restricted pathogen that causes typhoid fever. Even though it is a human-restricted pathogen, the bacterium is also isolated from environments such as groundwater and pond water. Here, we describe the genome sequence of the Salmonella enterica subsp. enterica serovar Typhi PM016/13 which was isolated from well water during a typhoid outbreak in Kelantan, Malaysia, in 2013.

Conventional polymerase chain reaction (PCR) testing requires many pipetting steps and has to be transported and stored in cold chain. To overcome these limitations, we designed a ready-to-use PCR test for Salmonella typhi using PCR reagents, primers against the ST50 gene of S. typhi, a built-in internal amplification control (IAC), and gel loading dye mixed and freeze-dried in a single tube. The 2-step dry-reagent-based assay was used to amplify a 1238-bp target gene and an 810-bp IAC gene from 73 BACTEC blood culture broths (33 true positives for S. typhi and 40 true negatives for non-S. typhi). The sensitivity, specificity, positive predictive value, and negative predictive value of the PCR assay were 87.9%, 100%, 100%, and 90.9%, respectively. We suggest that this rapid 2-step PCR test could be used for the rapid diagnosis of typhoid fever.

We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi B/SF/13/03/195 obtained from a typhoid carrier, who is a food handler in Pasir Mas, Kelantan.

An in-house loop-mediated isothermal amplification (LAMP) reaction was established and evaluated for sensitivity and specificity in detecting the presence of Salmonella Typhi (S. Typhi) isolates from Kelantan, Malaysia. Three sets of primers consisting of two outer and 4 inner were designed based on locus STBHUCCB_38510 of chaperone PapD of S. Typhi genes. The reaction was optimised using genomic DNA of S. Typhi ATCC7251 as the template. The products were visualised directly by colour changes of the reaction. Positive results were indicated by green fluorescence and negative by orange colour. The test was further evaluated for specificity, sensitivity and application on field samples. The results were compared with those obtained by gold standard culture method and Polymerase Chain Reaction (PCR). This method was highly specific and -10 times more sensitive in detecting S. Typhi compared to the optimised conventional polymerase chain reaction (PCR) method.

In this work we assessed the suitability of two different lipid membranes for the simulation of a TolC protein from Salmonella enterica serovar Typhi. The TolC protein family is found in many pathogenic Gram-negative bacteria including Vibrio cholera and Pseudomonas aeruginosa and acts as an outer membrane channel for expulsion of drug and toxin from the cell. In S. typhi, the causative agent for typhoid fever, the TolC outer membrane protein is an antigen for the pathogen. The lipid environment is an important modulator of membrane protein structure and function. We evaluated the conformation of the TolC protein in the presence of DMPE and POPE bilayers using molecular dynamics simulation. The S. typhi TolC protein exhibited similar conformational dynamics to TolC and its homologues. Conformational flexibility of the protein is seen in the C-terminal, extracellular loops, and α-helical region. Despite differences in the two lipids, significant similarities in the motion of the protein in POPE and DMPE were observed, including the rotational motion of the C-terminal residues and the partially open extracellular loops. However, analysis of the trajectories demonstrated effects of hydrophobic matching of the TolC protein in the membrane, particularly in the lengthening of the lipids and subtle movements of the protein’s β-barrel towards the lower leaflet in DMPE. The study exhibited the use of molecular dynamics simulation in revealing the differential effect of membrane proteins and lipids on each other. In this study, POPE is potentially a more suitable model for future simulation of the S. typhi TolC protein.

The detection and measurement of different antibody isotypes in the serum provide valuable indicators of the different stages of typhoid infection. Here, the ability of S. Typhi recombinant hemolysin E (HlyE) to detect multi-isotype antibody responses in sera of patients with typhoid and paratyphoid A was investigated using an indirect antibody immunoassay. Nanogram amounts of HlyE were found to be sufficient for detection of IgG and IgA isotypes and, in a study of individuals' sera (n = 100), the immunoassay was able to distinguish between typhoid and non-typhoid sera. The overall sensitivity, specificity and efficiency of the ELISA were 70% (39/56), 100% (44/44) and 83% respectively.

In our earlier study, an immunoblot analysis using sera from febrile patients revealed that a 50-kDa band from an outer membrane protein fraction of Salmonella enterica serovar Typhi was specifically recognized only by typhoid sera and not sera from other febrile illnesses. Here, we investigated the identities of the proteins contained in the immunogenic 50-kDa band to pinpoint antigens responsible for its immunogenicity. We first used LC-MS/MS for protein identification, then used the online tool ANTIGENpro for antigenicity prediction and produced recombinant proteins of the lead antigens for validation in an enzyme-linked immunosorbent assay (ELISA). We found that proteins TolC, GlpK and SucB were specific to typhoid sera but react to antibodies differently under native and denatured conditions. This difference suggests the presence of linear and conformational epitopes on these proteins.

Chronic carriers of Salmonella Typhi act as reservoirs for the organism and become the agents of typhoid outbreaks in a community. In this study, chronic carriers in Kelantan, Malaysia were first identified using the culture and polymerase chain reaction method. Then, a novel serological tool, designated Typhidot-C, was evaluated in retrospect using the detected individuals as control positives. Chronic carriage positive by the culture and polymerase chain reaction method was recorded at 3.6% (4 out of 110) among individuals who previously had acute typhoid fever and a 9.4% (10 out of 106) carriage rate was observed among food handlers screened during outbreaks. The Typhidot-C assay was able to detect all these positive carriers showing its potential as a viable carrier screening tool and can be used for efficient detection of typhoid carriers in an endemic area. These findings were used to establish the first carrier registry for S Typhi carriers in Malaysia.

Introduction Salmonella Paratyphi A (S. Paratyphi A) causes paratyphoid fever, a disease endemic in developing countries. It is transmitted via the faecal-oral route, mainly through contaminated food and water. The prevalence or incidence of the disease is increasing especially in China, India and Asia. Current diagnosis of S. Paratyphi A is via culture and molecular methods such as PCR. However, these methods do not offer a rapid, simple, and cost-effective detection of S. Paratyphi A especially for use in resource-limited settings. Objective The study was aimed at developing an in-house LAMP method as a rapid, sensitive, specific and cost-effective detection of S. Paratyphi A. Methods An In-house LAMP method was developed and optimized for the detection of S. Paratyphi A using primers that were designed based on intergenic region of SSPA1723a and SSPA1723 gene of S. Paratyphi A. The primers' specificity was tested on 60 bacteria strains consisting of 25 S. Paratyphi A, 20 other Salmonella serovars, and 15 non-Salmonella bacteria which were obtained from Institute for Research in Molecular Medicine (INFORMM) culture bank. Detection limit of LAMP was determined using 10-fold serial dilutions of S. Paratyphi A strain DNA and compared with culture and PCR results. The assay was further evaluated on 60 BACTEC blood culture broths suspected of S. Paratyphi A. The results were compared with those obtained by PCR assay and culture method. Results & Discussion In-house LAMP method was successfully established and optimized. The sensitivity of the assay was determined at 200 CFU. This LAMP assay gave positive result to all the 25 S. Paratyphi A isolates and negative to 20 other Salmonella and 15 non-Salmonella bacteria. This assay detected 8 samples as positive and 52 samples as negative for S. Paratyphi A. These results were similar to those results obtained by PCR assay and culture methods. Conclusion An in-house LAMP method was established in this study and could potentially be used as a rapid, sensitive, specific and cost-effective detection method for S. Paratyphi A especially in low-resource settings. However this LAMP method is only recommended for screening purposes and need to be further confirmed with gold standard method which is culture method and PCR.

Introduction Kelantan remains as the highest endemic area in Malaysia for typhoid cases with the incidence rate of 3.29 and 2.8 per 100,000 populations in 2008 and 2010. Salmonella Typhi is the causative pathogen of this illness which transmitted through fecal oral route, causing human is the only known reservoir for this organism. However, some typhoid cases related to contaminated water had also been reported. Objective To investigate the genetic diversity and relatedness of Salmonella Typhi isolated from water sample, and stool samples from food handlers and contacts in typhoid outbreak locality, Pasir Mas, Kelantan. Methods Nine Salmonella Typhi isolated from food handlers and contact while another one isolated from water sample were obtained from Makmal Kesihatan Awam Kota Bharu Kelantan between March to April 2013 and confirmed by biochemical test and serotyping. Pulsed field gel electrophoresis (PFGE) was performed according to CDC PulseNet Protocol and Bio-Rad CHEF MAPPER XA System. Dice Coefficient of Similarity (F value) was calculated for all isolates and a dendogram were constructed using Fingerprinting QuestTM software. The result was compared with previous data collected and interpreted according to the guidelines of Tenover et. al. (1995). Results & Discussion All nine isolates from food handlers and contacts showed similar PFGE pattern with the isolate from water sample, suggesting the disease was transmitted through water samples from well which is located in the typhoid outbreak area. Moreover, the PFGE pattern was unique and had never been found in S. Typhi previously isolated in Kelantan according to our PFGE database. Conclusion There are two possibilities of the source of the outbreak. The carriers among food handlers and contact might contaminated the water and causing the outbreak or vice versa.

Introduction S. Paratyphi A is a causative agent of paratyphoid fever with milder symptoms compared to typhoid fever. Culture method is the gold standard used for diagnosis and the disadvantages of the method is less sensitive, laborious and requires 3 – 5 days for identification of the bacteria. Therefore, a rapid and user-friendly asymmetric helicase-dependent amplification combined with lateral flow assay (HDA-LFA) was developed for the detection of S. Paratyphi A. Objectives To determine the detection limit, sensitivity and specificity of the HDA-LFA for the detection of S. Paratyphi A using spiked stool samples. Methods A pair of S. Paratyphi A HDA-LFA primer was designed to amplify a 93 bp intergenic region of S. Paratyphi A and a 123 bp competitive internal amplification control. The lateral flow strips were assembled after lining with antibodies using Biodot dispensing reagent. The asymmetric HDA assay was carried out using heating block for 1 hour at 65oC and the amplified products were then detected via LFA and analysed by naked eyes within 15 minutes. Results and discussion: The limit of detection for S. Paratyphi A HDA-LFA using spiked stool sample was at 10 2 CFU/ml while at 10 3 CFU/ml when using agarose gel electrophoresis method. The assay was also validated using stool samples spiked with 25 S. Paratyphi A and 75 non-S. Paratyphi A isolates and revealed 100% sensitivity and specificity without any inhibition. Conclusion The assay is found to be rapid, sensitive and specific and has the potential to be an alternative DNA-based detection method for laboratories with limited access to specific equipment such as thermal cycler.

Introduction Salmonella Typhi (S.Typhi) is a causative agent for typhoid fever, a major health problem especially in developing countries. In Malaysia, the disease is still an endemic with the occurrence of 1–4 cases per 100,000 populations reported from year 1996–2006. Early detection of the agent is important since immediate treatment given to the patients will save many lives. However, current methods for the diagnosis of S.Typhi did not satisfy the requirements for a rapid, simple, and cost-effective detection mode. Objective Our study is aimed to develop an in-house LAMP method for a rapid, sensitive, specific and cost-effective detection of S.Typhi. Methods An In-house method of LAMP was developed and optimized using genomic DNA of Salmonella Typhi ATCC7251. The test was further evaluated for its specificity, sensitivity and application on field samples. The result was compared with those obtained by PCR assay and culture method. Results & Discussion In-house LAMP method has been successfully developed and optimized. This LAMP method was shown to be more sensitive than PCR assay and highly specific where no cross-reactivity was observed with other tested bacteria. Results of LAMP on clinical samples were in accordance to the results obtained by PCR assay and culture method. Conclusion In-house LAMP method developed in this study can potentially be used as a rapid, sensitive, specific and cost-effective detection of Salmonella Typhi especially at low-resource settings. However, this LAMP method need to be further validated using larger number of clinical samples.

Introduction Salmonella Typhi is the causative agent for typhoid fever that infects people especially in underdeveloped and developing countries. Even though culture method is the gold standard for detection of this pathogen, there are some limitations such as time consuming and less sensitive that leads to the development of a more sensitive and efficient method such as polymerase chain reaction (PCR). Objective To evaluate the sensitivity of a multiplex PCR-DNA dipstick assay incomparison with culture method and EZTyphi Carrier DNA assay for the detection of S.Typhi in well water samples. Methods A total of 580 well water samples were collected and filtered using filter membrane. Bacteria trapped on the membrane was enriched in a selective Selenite F and evaluated using these three methods; (i) Culture method: Bacteria culture was plated on a selective media agar plate and further tested by biochemical tests and serotyping (test was performed within 3 days); (ii) EZTyphi Carrier DNA assay: Extracted DNA from bacteria culture was amplified using two sets of primers targeted for S. Typhi (1238 bp) and internal amplification control (IAC) (810 bp) (3 hours); (iii) Multiplex PCR-DNA dipstick assay: Extracted DNA was amplified using four sets of primers targeted for S. Typhi (70 bp), S. Paratyphi A (93 bp), pan-Salmonella (146 bp) and IAC (123 bp) (2 hours). Results & Discussion Fifteen out of 580 water samples were positive S.Typhi by multiplex PCR-DNA dipstick assay while one sample was positiveS. Typhi by EZTyphi Carrier DNA and culture method. This finding proved that the multiplex PCR-DNA dipstick was superior to culture method and PCR-agarose gel electrophoresis since it has higher positivity compared to the other two methods. Conclusion A rapid and sensitive multiplex PCR-DNA dipstick assay can be used to detect S. Typhi in well water especilally in typhoid endemic area.