Publications by authors named "Niyaz Ahmed"

171 Publications

Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase () Island.

mBio 2021 03 2;12(1). Epub 2021 Mar 2.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India

The genotoxin colibactin is a secondary metabolite produced by the polyketide synthase () island harbored by extraintestinal pathogenic (ExPEC) and other members of the that has been increasingly reported to have critical implications in human health. The present study entails a high-throughput whole-genome comparison and phylogenetic analysis of such pathogenic isolates to gain insights into the patterns of distribution, horizontal transmission, and evolution of the island. For the current study, 23 -positive ExPEC genomes were newly sequenced, and their virulome and resistome profiles indicated a preponderance of virulence encoding genes and a reduced number of genes for antimicrobial resistance. In addition, 4,090 genomes from the public domain were also analyzed for large-scale screening for -positive genomes, out of which a total of 530 positive genomes were studied to understand the subtype-based distribution pattern(s). The island showed a significant association with the B2 phylogroup (82.2%) and a high prevalence in sequence type 73 (ST73;  = 179) and ST95 ( = 110) and the O6:H1 ( = 110) serotype. Maximum-likelihood (ML) phylogeny of the core genome and intergenic regions (IGRs) of the ST95 model data set, which was selected because it had both -positive and -negative genomes, displayed clustering in relation to their carriage of the island. Prevalence patterns of genes encoding RM systems in the -positive and negative genomes were also analyzed to determine their potential role in island acquisition and the maintenance capability of the genomes. Further, the maximum-likelihood phylogeny based on the core genome and island sequences from 247 genomes with an intact island demonstrated horizontal gene transfer of the island across sequence types and serotypes, with few exceptions. This study vitally contributes to understanding of the lineages and subtypes that have a higher propensity to harbor the island-encoded genotoxin with possible clinical implications. Extraintestinal pathologies caused by highly virulent strains of amount to clinical implications with high morbidity and mortality rates. Pathogenic strains are evolving with the horizontal acquisition of mobile genetic elements, including pathogenicity islands such as the island, which produces the genotoxin colibactin, resulting in severe clinical outcomes, including colorectal cancer progression. The current study encompasses high-throughput comparative genomics and phylogenetic analyses to address the questions pertaining to the acquisition and evolution pattern of the genomic island in different subtypes. It is crucial to gain insights into the distribution, transfer, and maintenance of pathogenic islands, as they harbor multiple virulence genes involved in pathogenesis and clinical implications of the infection.
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http://dx.doi.org/10.1128/mBio.03634-20DOI Listing
March 2021

Cholesterol glucosylation-based survival strategy in Helicobacter pylori.

Helicobacter 2021 Apr 23;26(2):e12777. Epub 2020 Dec 23.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India.

Helicobacter pylori is a major chronic health problem, infecting more than half of the population worldwide. H. pylori infection is linked with various clinical complications ranging from gastritis to gastric cancer. The resolution of gastritis and peptic ulcer appears to be linked with the eradication of H. pylori. However, resistance to antibiotics and eradication failure rates are reaching alarmingly high levels. This calls for urgent action in finding alternate methods for H. pylori eradication. Here, we discuss the recently identified mechanism of H. pylori known as cholesterol glucosylation, mediated by the enzyme cholesterol-α-glucosyltransferase, encoded by the gene cgt. Cholesterol glucosylation serves several functions that include promoting immune evasion, enhancing antibiotic resistance, maintaining the native helical morphology, and supporting functions of prominent virulence factors such as CagA and VacA. Consequently, strategies aiming at inhibition of the cholesterol glucosylation process have the potential to attenuate the potency of H. pylori infection and abrogate H. pylori immune evasion capabilities. Knockout of H. pylori cgt results in unsuccessful colonization and elimination by the host immune responses. Moreover, blocking cholesterol glucosylation can reverse antibiotic susceptibility in H. pylori. In this work, we review the main roles of cholesterol glucosylation in H. pylori and evaluate whether this mechanism can be targeted for the development of alternate methods for eradication of H. pylori infection.
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http://dx.doi.org/10.1111/hel.12777DOI Listing
April 2021

Whole-Genome Analysis of Clinical Vibrio cholerae O1 in Kolkata, India, and Dhaka, Bangladesh, Reveals Two Lineages of Circulating Strains, Indicating Variation in Genomic Attributes.

mBio 2020 11 10;11(6). Epub 2020 Nov 10.

Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.

serogroup O1 is responsible for epidemic and pandemic cholera and remains a global public health threat. This organism has been well established as a resident flora of the aquatic environment that alters its phenotypic and genotypic attributes for better adaptation to the environment. To reveal the diversity of clinical isolates of O1 in the Bay of Bengal, we performed whole-genome sequencing of isolates from Kolkata, India, and Dhaka, Bangladesh, collected between 2009 and 2016. Comparison with global isolates by phylogenetic analysis placed the current isolates in two Asian lineages, with lineages 1 and 2 predominant in Dhaka and Kolkata, respectively. Each lineage possessed different genetic traits in the cholera toxin B subunit gene, seventh pandemic island II, integrative and conjugative element, and antibiotic-resistant genes. Thus, although recent global transmission of O1 from South Asia has been attributed only to isolates of lineage 2, another distinct lineage exists in Bengal. Cholera continues to be a global concern, as large epidemics have occurred recently in Haiti, Yemen, and countries of sub-Saharan Africa. A single lineage of O1 has been considered to be introduced into these regions from South Asia and to cause the spread of cholera. Using genomic epidemiology, we showed that two distinct lineages exist in Bengal, one of which is linked to the global lineage. The other lineage was found only in Iran, Iraq, and countries in Asia and differed from the global lineage regarding cholera toxin variant and drug resistance profile. Therefore, the potential transmission of this lineage to other regions would likely cause worldwide cholera spread and may result in this lineage replacing the current global lineage.
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http://dx.doi.org/10.1128/mBio.01227-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7667034PMC
November 2020

A comparative whole genome analysis of Helicobacter pylori from a human dense South Asian setting.

Helicobacter 2021 Feb 18;26(1):e12766. Epub 2020 Oct 18.

The Hospital for Tropical Diseases, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.

Helicobacter pylori, a Gram-negative bacterium, is associated with a wide range of gastric diseases such as gastritis, duodenal ulcer, and gastric cancer. The prevalence of H pylori and risk of disease vary in different parts of the world based on the prevailing bacterial lineage. Here, we present a contextual and comparative genomics analysis of 20 clinical isolates of H pylori from patients in Bangladesh. Despite a uniform host ethnicity (Bengali), isolates were classified as being part of the HpAsia2 (50%) or HpEurope (50%) population. Out of twenty isolates, eighteen isolates were cagA positive, with two HpEurope isolates being cagA negative, three EPIYA motif patterns (AB, AB-C, and ABC-C) were observed among the cagA-positive isolates. Three vacA genotypes were observed with the s1m1i1dic1 genotype observed in 75% of isolates; the s1m2i1d1c2 and s2m2i2d2c2 genotypes were found to be 15% and 10% of isolates, respectively. The non-virulent genotypes s2m2i2d2c2 was only observed in HpEurope population isolates. Genotypic analysis of oipA gene, present in all isolates, revealed five different patterns of the CT repeat; all HpAsia2 isolates were in "ON" while 20% of HpEurope isolates were genotypically "OFF." The three blood group antigen binding adhesins encoded genes (bab genes) examined and we observed that the most common genotype was (babA/babB/-) found in eight isolates, notably six were HpAsia2 isolates. The babA gene was found in all HpAsia2 isolates but present in only half of the HpEurope isolates. In silico antibiotic susceptibility analysis revealed that 40% of the strains were multi-drug resistant. Mutations associated with resistance to metronidazole, fluoroquinolone, and clarithromycin were detected 90%, 45%, and 5%, respectively, in H pylori strain. In conclusion, it is evident that two populations of H pylori with similar antibiotic profiles are predominant in Bangladesh, and it appears that genotypically the HpAisa2 isolates are potentially more virulent than the HpEurope isolates.
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http://dx.doi.org/10.1111/hel.12766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7816255PMC
February 2021

Design of an inhibitor of Helicobacter pylori cholesteryl-α-glucoside transferase critical for bacterial colonization.

Helicobacter 2020 Oct 15;25(5):e12720. Epub 2020 Jul 15.

International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka.

Background: Fifty percent of the world's population surves as a host for Helicobacter pylori, gastric cancer causing bacteria, that colonizes the gastric region of digestive tract. It has a remarkable capacity to infect the host stomach for the entire lifetime despite an activated host immune response.

Methods: In this study, we have performed the virtual screening analysis of protein-inhibitor binding between the glycosyl transferase enzymes of Helicobacter pylori (CapJ or HP0421) and a corresponding library of inhibitors in the known substrate-binding pockets. We have docked our library of ligands consisting of cholesterol backbone with CapJ protein and identified several ligands' interacting amino acid residues present in active site pocket(s) of the protein.

Results: In most of the cases, the ligands showed an interaction with the residues of the same pocket of the enzyme. Top three (03) hits were filtered out from the whole data set, which might act as potent inhibitors of the enzyme-substrate reaction.

Conclusions: This study describes a new possibility by which colonization of H. pylori can be limited. The reported evidence suggests that comprehensive knowledge and wet laboratory validation of these inhibitors are needed in order to develop them as lead molecules.
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http://dx.doi.org/10.1111/hel.12720DOI Listing
October 2020

Extended-Spectrum Beta-Lactamase-Producing in Drinking Water Samples From a Forcibly Displaced, Densely Populated Community Setting in Bangladesh.

Front Public Health 2020 18;8:228. Epub 2020 Jun 18.

International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.

Community-acquired infections due to extended-spectrum beta-lactamase (ESBL) producing are rising worldwide, resulting in increased morbidity, mortality, and healthcare costs, especially where poor sanitation and inadequate hygienic practices are very common. This study was conducted to investigate the prevalence and characterization of multidrug-resistant (MDR) and ESBL-producing in drinking water samples collected from Rohingya camps, Bangladesh. A total of 384 isolates were analyzed in this study, of which 203 were from household or point-of-use (POU) water samples, and 181 were from source water samples. The isolates were tested for virulence genes, ESBL-producing genes, antimicrobial susceptibility by VITEK 2 assay, plasmid profiling, and conjugal transfer of AMR genes. Of the 384 isolates tested, 17% (66/384) were found to be ESBL producers. The abundance of ESBL-producers in source water contaminated with was observed to be 14% (27/181), whereas, 19% (39/203) ESBL producers was found in household POU water samples contaminated with . We detected 71% (47/66) ESBL to be MDR. Among these 47 MDR isolates, 20 were resistant to three classes, and 27 were resistant to four different classes of antibiotics. Sixty-four percent (42/66) of the ESBL producing carried 1 to 7 plasmids ranging from 1 to 103 MDa. Only large plasmids with antibiotic resistance properties were found transferrable via conjugation. Moreover, around 7% (29/384) of isolates harbored at least one of 10 virulence factors belonging to different pathotypes. The findings of this study suggest that the drinking water samples analyzed herein could serve as an important source for exposure and dissemination of MDR, ESBL-producing and pathogenic lineages, which therewith pose a health risk to the displaced Rohingya people residing in the densely populated camps of Bangladesh.
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http://dx.doi.org/10.3389/fpubh.2020.00228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314906PMC
May 2021

Genome Dynamics of Vibrio cholerae Isolates Linked to Seasonal Outbreaks of Cholera in Dhaka, Bangladesh.

mBio 2020 02 11;11(1). Epub 2020 Feb 11.

International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh

The temporal switching of serotypes from serotype Ogawa to Inaba and back to Ogawa was identified in O1, which was responsible for seasonal outbreaks of cholera in Dhaka during the period 2015 to 2018. In order to delineate the factors responsible for this serotype transition, we performed whole-genome sequencing (WGS) of O1 multidrug-resistant strains belonging to both the serotypes that were isolated during this interval where the emergence and subsequent reduction of the Inaba serotype occurred. The whole-genome-based phylogenetic analysis revealed clonal expansion of the Inaba isolates mainly responsible for the peaks of infection during 2016 to 2017 and that they might have evolved from the prevailing Ogawa strains in 2015 which coclustered with them. Furthermore, the gene in these Inaba serotype isolates was inactivated due to insertion of a transposable element at the same position signifying the clonal expansion. Also, isolates in the Inaba serotype dominant clade mainly contained classical allele and revealed differences in the genetic composition of eventh andemic sland II (VSP-II) and the SXT integrative and conjugative element (SXT-ICE) compared to those of Ogawa serotype strains which remerged in 2018. The variable presence of phage-inducible chromosomal island-like element 1 (PLE1) was also noted in the isolates of the Inaba serotype dominant clade. The detailed genomic characterization of the sequenced isolates has shed light on the forces which could be responsible for the periodic changes in serotypes of and has also highlighted the need to analyze the mobilome in greater detail to obtain insights into the mechanisms behind serotype switching. The switching of serotype from Ogawa to Inaba and back to Ogawa has been observed temporally in O1, which is responsible for endemic cholera in Bangladesh. The serospecificity is key for effective intervention and for preventing cholera, a deadly disease that continues to cause significant morbidity and mortality worldwide. In the present study, WGS of allowed us to better understand the factors associated with the serotype switching events observed during 2015 to 2018. Genomic data analysis of strains isolated during this interval highlighted variations in the genes , , and and also identified significant differences in the genetic content of the mobilome, which included key elements such as SXT ICE, VSP-II, and PLE. Our results indicate that selective forces such as antibiotic resistance and phage resistance might contribute to the clonal expansion and predominance of a particular serotype responsible for an outbreak.
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http://dx.doi.org/10.1128/mBio.03339-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7018647PMC
February 2020

Colistin-resistant carrying in food, water, hand rinse, and healthy human gut in Bangladesh.

Gut Pathog 2020 27;12. Epub 2020 Jan 27.

1Infectious Diseases Division (IDD), International Centre for Diarrheal Disease Research (icddr,b), 68, Shaheed Tajuddin Ahmed Sharani, Dhaka, 1212 Bangladesh.

Background: One of the most significant public health concerns in today's world is the persistent upsurge of infections caused by multidrug resistant bacteria. As a result, clinicians are being forced to intervene with either less effective backup drugs or ones with substantial side-effects. Colistin is a last resort antimicrobial agent for the treatment of infections caused by multi-drug resistant gram-negative bacteria.

Methods: (n = 65) isolated from street food (n = 20), hand rinse (n = 15), surface water (n = 10), and healthy human stool (n = 20) were tested for colistin resistance gene and response to antimicrobial agents. Antimicrobial resistance genes and virulence genes were detected by employing polymerase chain reaction. DNA fingerprinting of the strains were determined by pulsed-field gel electrophoresis.

Results: Screening of allowed us to confirm colistin resistance marker gene 1 in 13 strains (street food, n = 4; hand rinse, n = 2; surface water, n = 4; and stool, n = 3); and two of these strains carrying -1 harbored gene encoding extended spectrum beta lactamase. Antibiotic assay results revealed all 13 strains carrying -1 to be multi-drug resistant (MDR), including to colistin. The minimum inhibitory concentration (MIC) for colistin ranged from 2 to 6 μg/ml. DNA sequencing confirmed homogeneity of the nucleotide sequence for , but the strains were heterogenous, as confirmed by pulsed-field gel electrophoresis suggesting horizontal transmission of colistin resistance in Bangladesh.

Conclusion: Widespread dissemination of strains carrying -1 encoding resistance to colistin in the present study is alarming as this is the last resort drug for the treatment of infections caused by MDR gram-negative bacteria resistant to almost all drugs used commonly.
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http://dx.doi.org/10.1186/s13099-020-0345-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986151PMC
January 2020

Quantification of Airborne Resistant Organisms With Temporal and Spatial Diversity in Bangladesh: Protocol for a Cross-Sectional Study.

JMIR Res Protoc 2019 Dec 19;8(12):e14574. Epub 2019 Dec 19.

Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.

Background: Antimicrobial resistance is a widespread, alarming issue in global health and a significant contributor to human death and illness, especially in low and middle-income countries like Bangladesh. Despite extensive work conducted in environmental settings, there is a scarcity of knowledge about the presence of resistant organisms in the air.

Objective: The objective of this protocol is to quantify and characterize the airborne resistomes in Bangladesh, which will be a guide to identify high-risk environments for multidrug-resistant pathogens with their spatiotemporal diversity.

Methods: This is a cross-sectional study with an environmental, systematic, and grid sampling strategy focused on collecting air samples from different outdoor environments during the dry and wet seasons. The four environmental compartments are the frequent human exposure sites in both urban and rural settings: urban residential areas (n=20), live bird markets (n=20), rural households (n=20), and poultry farms (n=20). We obtained air samples from 80 locations in two seasons by using an active microbial air sampler. From each location, five air samples were collected in different media to yield the total bacterial count of 3rd generation cephalosporin (3GC) resistant Enterobacteriaceae, carbapenem-resistant Enterobacteriaceae, vancomycin-resistant Enterococci and methicillin-resistant Staphylococcus aureus.

Results: The study started in January 2018, and the collection of air samples was completed in November 2018. We have received 800 air samples from 80 study locations in both dry and wet seasons. Currently, the laboratory analysis is ongoing, and we expect to receive the preliminary results by October 2019. We will publish the complete result as soon as we clean and analyze the data and draft the manuscript.

Conclusions: The existence of resistant bacteria in the air like those producing extended-spectrum beta-lactamases, carbapenem-resistant Enterobacteriaceae, vancomycin-resistant Enterococci, and methicillin-resistant Staphylococcus aureus will justify our hypothesis that the outdoor environment (air) in Bangladesh acts as a reservoir for bacteria that carry genes conferring resistance to antibiotics. To our knowledge, this is the first study to explore the presence of superbugs in the air in commonly exposed areas in Bangladesh.

International Registered Report Identifier (irrid): DERR1-10.2196/14574.
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http://dx.doi.org/10.2196/14574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6940864PMC
December 2019

Genomic and Functional Characterization of Poultry From India Revealed Diverse Extended-Spectrum β-Lactamase-Producing Lineages With Shared Virulence Profiles.

Front Microbiol 2019 3;10:2766. Epub 2019 Dec 3.

International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

Extended-spectrum β-lactamases (ESBLs) form the most important resistance determinants prevalent worldwide. Data on ESBL-producing from poultry and livestock are scarce in India. We present data on the functional and genomic characterization of ESBL-producing obtained from poultry in India. The whole genome sequences of 28 ESBL-producing were analyzed comprising of 12 broiler chicken isolates, 11 free-range chicken isolates, and 5 human extraintestinal pathogenic . All of the 28 ESBL-producing isolates were tested for antibiotic susceptibilities, conjugation, and virulence-associated phenotypic characteristics. A total of 13 sequence types were identified from the poultry , which included globally successful sequence types such as ST117 (9%), ST131 (4.3%), and ST10 (4.3%). The most common ESBL gene detected in poultry genomes was (17%). Also, FIB (73%) and FII (73%) were the most common plasmid replicons identified. Conjugation experiments demonstrated 54 (7/13), 30 (3/10), and 40% (2/5) of broiler, free-range, and human ExPEC to be able to transfer their ESBL genes, respectively. The virulence-associated phenotypic tests revealed the broiler, free-range, and human ExPEC isolates to be comparable in biofilm formation, resistance to serum bactericidal activity, adherence, and invasion capabilities. Our overall results showed prevalence of virulence phenotypes among the diverse ESBL-producing from poultry; while certain clones from broiler-poultry may indeed have the potential to cause infection in humans.
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http://dx.doi.org/10.3389/fmicb.2019.02766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901389PMC
December 2019

Prevalence of in Bangladesh: Isolation and Characterization of a Rare Phage MK-13 That Can Robustly Identify Shigellosis Caused by Type 1.

Front Microbiol 2019 7;10:2461. Epub 2019 Nov 7.

International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

Shigellosis, caused by type 1, is understudied and underreported. For 3 years, GEMS study identified 5.4% of all as . We showed the prevalent serotypes of in Bangladesh and phage-based diagnosis of type 1, a rapid and low-cost approach. Previously typed 793 clinical strains were used for serotype distribution. Twenty-eight environmental water samples were collected for isolation of phages. Forty-eight serotypes of and other enteric bacteria were used for testing the susceptibility to phage MK-13. Electron microscopy, restriction enzyme analysis, whole genome sequencing (WGS), and annotation were performed for extensive characterization. type 1 is the second most prevalent serotype among 20 serotypes of in Bangladesh. We isolated a novel phage, MK-13, which specifically lyses type 1, but doesn't lyse other 47 serotypes of or other enteric bacteria tested. The phage belongs to the family and distinct from other phages indicated by electron microscopy and restriction enzyme analysis, respectively. MK-13 genome consists of 158 kbp of circularly permuted double-stranded DNA with G + C content of 49.45%, and encodes 211 open reading frames including four tRNA-coding regions. The genome has 98% identity with previously reported phage, ΦSboM-AG3, reported to have a broader host range infecting most of the and other species of tested. To our knowledge, MK-13 is the first phage reported to be used as a diagnostic marker to detect type 1, especially in remote settings with limited laboratory infrastructure.
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http://dx.doi.org/10.3389/fmicb.2019.02461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853846PMC
November 2019

Occurrence of and faecal coliforms in drinking water at source and household point-of-use in Rohingya camps, Bangladesh.

Gut Pathog 2019 1;11:52. Epub 2019 Nov 1.

1International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, 1212 Bangladesh.

Background: Safe water is essential for life but unsafe for human consumption if it is contaminated with pathogenic microorganisms. An acceptable quality of water supply (adequate, safe and accessible) must be ensured to all human beings for a healthy life.

Methods: We collected and analyzed a total of 12,650 drinking water samples, for the presence of and faecal coliforms, from a large habitation of the displaced Rohingya population comprising of about 1.16 million people living within 4 km.

Results: We found that 28% (n = 893) water samples derived from tubewells were contaminated with faecal coliforms and 10.5% (n = 333) were contaminated with ; also, 73.96% (n = 4644) samples from stored household sources (at point of use-POU) were found contaminated with faecal coliforms while 34.7% (n = 2179) were contaminated with It was observed that a higher percentage of POU samples fall in the highest risk category than that of their corresponding sources.

Conclusions: From our findings, it appears that secondary contamination could be a function of very high population density and could possibly occur during collection, transportation, and storage of water due to lack of knowledge of personal and domestic hygiene. Hence, awareness campaign is necessary, and the contaminated sources should be replaced. Further, the POU water should be treated by a suitable method.
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http://dx.doi.org/10.1186/s13099-019-0333-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824040PMC
November 2019

Mycobacterium tuberculosis DosR regulon gene Rv2004c contributes to streptomycin resistance and intracellular survival.

Int J Med Microbiol 2019 Dec 30;309(8):151353. Epub 2019 Aug 30.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, 500046, India; Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh. Electronic address:

Tuberculosis (TB) is the deadly infectious disease challenging the public health globally and its impact is further aggravated by co-infection with HIV and the emergence of drug resistant strains of Mycobacterium tuberculosis. In this study, we attempted to characterise the Rv2004c encoded protein, a member of DosR regulon, for its role in drug resistance. In silico docking analysis revealed that Rv2004c binds with streptomycin (SM). Phosphotransferase assay demonstrated that Rv2004c possibly mediates SM resistance through the aminoglycoside phosphotransferase activity. Further, E. coli expressing Rv2004c conferred resistance to 100μM of SM in liquid broth cultures indicating a mild aminoglycoside phosphotransferase activity of Rv2004c. Moreover, we investigated the role of MSMEG_3942 (an orthologous gene of Rv2004c) encoded protein in intracellular survival, its effect on in-vitro growth and its expression in different stress conditions by over expressing it in Mycobacterium smegmatis (M. smegmatis). MSMEG_3942 overexpressing recombinant M. smegmatis strains grew faster in acidic medium and also showed higher bacillary counts in infected macrophages when compared to M. smegmatis transformed with vector alone. Our results are likely to contribute to the better understanding of the involvement of Rv2004c in partial drug resistance, intracellular survival and adaptation of bacilli to stress conditions.
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http://dx.doi.org/10.1016/j.ijmm.2019.151353DOI Listing
December 2019

Environmental reservoirs of Vibrio cholerae.

Vaccine 2020 02 5;38 Suppl 1:A52-A62. Epub 2019 Jul 5.

International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh.

The environmental reservoir of Vibrio cholerae, the causative agent of cholera, has been a topic of scientific investigation ever since the discovery of the bacterium itself. While the bacteria can be isolated from both clinical and environmental sources during epidemics, it evades isolation by conventional culture techniques during the period between successive epidemics. The problem is identifying the location and mode of survival and multiplication of V. cholerae during this inter-epidemic period. This information is crucial not only for epidemiological reasons, but also because the seasonality of cholera epidemics is plausibly mediated by the climate-regulated activity of the reservoir. This article focuses on the epidemiological importance of the environmental reservoir of V. cholerae, considering several investigations made on different types of aquatic fauna (zooplanktons, crustaceans, etc.) and flora (macrophytes and microphytes). After evaluating different lines of evidence, we make the case that certain species of cyanobacteria (Anabaena variabilis, Microcystis aeruginosa) can act as inter-epidemic reservoirs of V. cholerae. Physiological and functional aspects of this association are also discussed. We then present a hypothesis, expanding upon a previously published conceptual model, of how the climate-regulated seasonality of cholera epidemics is mediated by the effect of climatic factors on algal bloom and other local abiotic variables in the water, using Bangladesh as a model. Finally, another aspect of the climate-dependence of disease patterns is briefly explored: large-scale environmental signatures associated with cholera, and recent modelling efforts to predict cholera outbreaks based on coastal phytoplankton. The review, therefore, serves not only as a study of the identity of the inter-epidemic reservoir of V. cholerae, but also explores different ways in which the reservoir and the pathogen behaviour is affected by the climate, and the possible consequences it may have on disease pattern.
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http://dx.doi.org/10.1016/j.vaccine.2019.06.033DOI Listing
February 2020

Occurrence and Characterization of Methicillin Resistant in Processed Raw Foods and Ready-to-Eat Foods in an Urban Setting of a Developing Country.

Front Microbiol 2019 14;10:503. Epub 2019 Mar 14.

Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands.

Infections by methicillin-resistant (MRSA) are gradually increasing in the community. In this study, we investigated a total of 162 food samples including 112 ready-to-eat (RTE) foods and 40 processed raw meat and fish samples collected from retail vendors in Dhaka, Bangladesh and determined the occurrence of toxigenic and MRSA. Around 22% of samples were positive for , RTE foods being more positive (23%) than the processed raw meat/fish samples (18%). Among 35 isolates, 74% were resistant to erythromycin, 49% to ciprofloxacin and around 30% to oxacillin and cefoxitin. Around 37% of isolates were resistant to ≥3 classes of antibiotics and 26% of isolates ( = 9) were identified as MRSA. Majority of the isolates were positive for enterotoxin genes (74%), followed by gene (71%), toxic shock syndrome toxin () gene (17%) and exfoliative toxin genes (11%). Multi locus sequence typing (MLST) of 9 MRSA isolates identified four different types such as ST80 ( = 3), ST6 ( = 2), ST239 ( = 2) and ST361 ( = 2). typing of MRSA isolates revealed seven different types including t1198 ( = 2), t315 ( = 2), t037 ( = 1), t275 ( = 1), t304 ( = 1), t8731 ( = 1) and t10546 ( = 1). To our knowledge, this is the first report entailing baseline data on the occurrence of MRSA in RTE foods in Dhaka highlighting a potential public health risk to street food consumers.
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http://dx.doi.org/10.3389/fmicb.2019.00503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426745PMC
March 2019

Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Lineage Sequence Type 648.

Antimicrob Agents Chemother 2019 06 24;63(6). Epub 2019 May 24.

Institute of Microbiology and Epizootics, Free University Berlin, Berlin, Germany

The pathogenic extended-spectrum-beta-lactamase (ESBL)-producing lineage ST648 is increasingly reported from multiple origins. Our study of a large and global ST648 collection from various hosts (87 whole-genome sequences) combining core and accessory genomics with functional analyses and experiments suggests that ST648 is a nascent and generalist lineage, lacking clear phylogeographic and host association signals. By including large numbers of ST131 ( = 107) and ST10 ( = 96) strains for comparative genomics and phenotypic analysis, we demonstrate that the combination of multidrug resistance and high-level virulence are the hallmarks of ST648, similar to international high-risk clonal lineage ST131. Specifically, our , , and results demonstrate that ST648 is well equipped with biofilm-associated features, while ST131 shows sophisticated signatures indicative of adaption to urinary tract infection, potentially conveying individual ecological niche adaptation. In addition, we used a recently developed NFDS (negative frequency-dependent selection) population model suggesting that ST648 will increase significantly in frequency as a cause of bacteremia within the next few years. Also, ESBL plasmids impacting biofilm formation aided in shaping and maintaining ST648 strains to successfully emerge worldwide across different ecologies. Our study contributes to understanding what factors drive the evolution and spread of emerging international high-risk clonal lineages.
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http://dx.doi.org/10.1128/AAC.00243-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535536PMC
June 2019

Molecular Genetic and Functional Analysis of -Harboring, Extra-Intestinal Pathogenic From India.

Front Microbiol 2018 15;9:2631. Epub 2018 Nov 15.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India.

Colibactin, a genotoxin, encoded by the pathogenicity island of belonging to the B2 phylogroup has been reported as a determinant of bacterial pathogenicity. The present study was carried out to detect the pathogenicity island in extraintestinal pathogenic (ExPEC) isolated from a tertiary hospital in Pune, India. Of 462 isolates analyzed, the genomic island was detected in 35 (7.6%) isolates, which predominantly belonged to pathogenic phylogroup B2 (97%), and harbored virulence genes such as , and . Biofilm formation assay revealed 21 of the 35 carrying isolates to be strong (SBF > 1.0), 10 isolates to be moderate (SBF = 0.5-1.0), and 4 as weak (SBF < 0.5) biofilm formers. All of the carrying isolates proved resistant against bactericidal activity of human serum. Assays carried out to detect antimicrobial susceptibility revealed 11% of these isolates to be multidrug resistant, 37% producing ESBL and 25% were positive for . The observed prevalence of multidrug resistance and colibactin producing characteristics among pathogenic belonging to phylogenetic group B2 advocate urgent need for broader surveillance in order to understand and prevent transmission of these ExPEC in community and hospital settings.
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http://dx.doi.org/10.3389/fmicb.2018.02631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249908PMC
November 2018

Roles of Cholesteryl-α-Glucoside Transferase and Cholesteryl Glucosides in Maintenance of Helicobacter pylori Morphology, Cell Wall Integrity, and Resistance to Antibiotics.

mBio 2018 11 27;9(6). Epub 2018 Nov 27.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India

Infection of the human stomach caused by is very common, as the pathogen colonizes more than half of the world's population. It is associated with varied outcomes of infection, such as peptic ulcer disease, gastric ulcers, and mucosa-associated lymphoid tissue lymphoma, and is generally considered a risk factor for the development of gastric adenocarcinoma. Cholesteryl glucosides (CGs) constitute a vital component of the cell wall of and contribute to its pathogenicity and virulence. The gene, which encodes cholesteryl-α-glucoside transferase (CGT), appears critical for the enzymatic function of integrating unique CGs into the cell wall of , and deletion of this gene leads to depletion of CGs and their variants. Herein, we report that the deletion of and consequent deficiency of cholesterol alter the morphology, shape, and cell wall composition of cells, as demonstrated by high-resolution confocal microscopy and flow cytometry analyses of two different type strains of , their isogenic knockouts as well as a reconstituted strain. Moreover, measurement of ethidium bromide (EtBr) influx by flow cytometry showed that lack of CGs increased cell wall permeability. Antimicrobial susceptibility testing revealed that the isogenic knockout strains ( and ) were sensitive to antibiotics, such as fosfomycin, polymyxin B, colistin, tetracycline, and ciprofloxacin, in contrast to the wild-type strains that were resistant to the above antibiotics and tended to form denser biofilms. Lipid profile analysis of both and strains showed an aberrant profile of lipopolysaccharides (LPS) in the strain. Taken together, we herein provide a set of mechanistic evidences to demonstrate that CGs play critical roles in the maintenance of the typical spiral morphology of and its cell wall integrity, and any alteration in CG content affects the characteristic morphological features and renders the susceptible to various antibiotics. is an important cause of chronic gastritis leading to peptic ulcer and is a major risk factor for gastric malignancies. Failure in the eradication of infection and increasing antibiotic resistance are two major problems in preventing colonization. Hence, a deeper understanding of the bacterial survival strategies is needed to tackle the increasing burden of infection by an appropriate intervention. Our study demonstrated that the lack of cholesteryl glucosides (CGs) remarkably altered the morphology of and increased permeability of the bacterial cell wall. Further, this study highlighted the substantial role of CGs in maintaining the typical morphology that is essential for retaining its pathogenic potential. We also demonstrated that the loss of CGs in renders the bacterium susceptible to different antibiotics.
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http://dx.doi.org/10.1128/mBio.01523-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282200PMC
November 2018

ESBL-plasmid carriage in enhances in vitro bacterial competition fitness and serum resistance in some strains of pandemic sequence types without overall fitness cost.

Gut Pathog 2018 15;10:24. Epub 2018 Jun 15.

1Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, Robert-von-Ostertag Str. 7-13, 14163 Berlin, Germany.

Background: Extended spectrum beta lactamase (ESBL)-producing extraintestinal pathogenic infections are of global interest because of their clinical and economic impact. The ESBL resistance genes disseminate through plasmids, and are found in successful global lineages such as ST131 and ST648. The carriage of plasmids has been suggested to result in a fitness burden, but recently it was shown that ESBL-plasmids enhanced virulence in pandemic ST131 and ST648 lineages without affecting their fitness. Herein, we investigated the influence of ESBL-plasmids on bacterial competition and serum resistance, both of which are essential characteristics of ExPEC during infections.

Methods: Triplets of ESBL-plasmid-carrying wildtype (WT), plasmid-cured variant (PCV) and transformant (T) of five ExPEC strains of ST131 and ST648 were used for bacterial competition experiments with colicin-producing commensal , competitive adhesion experiments and serum survival. In addition, resilience after SDS, acid, osmotic challenges and RNA sequence data were analyzed.

Results: In all five strains tested, ESBL-plasmid carriage did not negatively influence fitness in direct bacterial competition with commensal in vitro. That is, WTs did not show any disadvantages when compared to their isogenic plasmid-free PCV. For one strain we even found the opposite as PCV17433 was out-competed by a commensal strain, which suggests an even protective role of the ESBL-plasmid carried by the WT17433. Similarly, in the serum-resistance experiments, the PCVs of two strains (PCV17433 and PCV17887) were more sensitive to serum, unlike WTs and Ts. The observed inter-strain differences could be explained by the different genetic content of plasmids carried in those strains.

Conclusions: Overall, we found no compelling evidence for an increased burden resulting from the carriage of ESBL-plasmids in the absence of antimicrobial selection pressure in the strains of pandemic ST131 and ST648; rather, the possession of certain ESBL-plasmids was beneficial for some strains in regarding competition fitness and serum survival.
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http://dx.doi.org/10.1186/s13099-018-0243-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003029PMC
June 2018

Author Correction: Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis.

Sci Rep 2018 May 15;8(1):7892. Epub 2018 May 15.

Robert Koch Institute, Berlin, 13353, Germany.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
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http://dx.doi.org/10.1038/s41598-018-25809-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5951889PMC
May 2018

Inactivation of nuclear factor κB by MIP-based drug combinations augments cell death of breast cancer cells.

Drug Des Devel Ther 2018 1;12:1053-1063. Epub 2018 May 1.

Institute of Biological Science (Genetics & Molecular Biology), Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.

Background: Drug combination therapy to treat cancer is a strategic approach to increase successful treatment rate. Optimizing combination regimens is vital to increase therapeutic efficacy with minimal side effects.

Materials And Methods: In the present study, we evaluated the in vitro cytotoxicity of double and triple combinations consisting of 1'S-1'-acetoxychavicol acetate (ACA), (MIP) and cisplatin (CDDP) against 14 various human cancer cell lines to address the need for more effective therapy. Our data show synergistic effects in MCF-7 cells treated with MIP:ACA, MIP:CDDP and MIP:ACA:CDDP combinations. The type of interaction between MIP, ACA and CDDP was evaluated based on combination index being <0.8 for synergistic effect. Identifying the mechanism of cell death based on previous studies involved intrinsic apoptosis and nuclear factor kappa B (NF-κB) and tested in Western blot analysis. Inactivation of NF-κB was confirmed by p65 and IκBα, while intrinsic apoptosis pathway activation was confirmed by caspase-9 and Apaf-1 expression.

Results: All combinations confirmed intrinsic apoptosis activation and NF-κB inactivation.

Conclusion: Double and triple combination regimens that target induction of the same death mechanism with reduced dosage of each drug could potentially be clinically beneficial in reducing dose-related toxicities.
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http://dx.doi.org/10.2147/DDDT.S141925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5935191PMC
September 2018

Microbiological quality assessment of milk at different stages of the dairy value chain in a developing country setting.

Int J Food Microbiol 2018 Aug 17;278:11-19. Epub 2018 Apr 17.

Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka 1212, Bangladesh.

The main objective of the study was to assess the microbiological quality of milk at different stages of the dairy value chain from farm to the factory in Bangladesh. A total of 438 raw milk samples (387 from primary producers, 32 from collectors, 15 from chilling plants, 4 from local restaurants) and 95 commercially processed milk samples were collected from northern part of Bangladesh. Almost 72% (n = 280) of samples at producer level and 100% from both collectors (n = 32) and chilling plants (n = 15) were contaminated with coliforms while 57% (n = 220) of samples from producers, 91% (n = 29) of samples from collectors and 100% (n = 15) from chilling plants were contaminated with fecal coliforms. Around 31% (n = 119) of samples from producers were positive for E. coli whereas >60% (n = 20) and 100% (n = 15) samples from collectors and chilling plants, respectively were positive for E. coli. One quarter of samples from collectors were positive for B. cereus and coagulase positive staphylococci and 33% (n = 5) of samples from chilling plants were positive for both of these microorganisms. In case of commercially processed milk, 77% (n = 46) and 37% (n = 22) of pasteurized milk samples had a high aerobic plate count (APC) (10 CFU/ml) and coliform count (>10 CFU/ml), respectively. None of the samples was positive for Shigella spp., Salmonella spp., and Campylobacter spp. Among 158 E. coli positive raw milk samples, 9% (n = 14) contained pathogenic E. coli, and enteroaggregative E. coli (EAEC) and Shiga-toxin producing E. coli (STEC) were found to be the predominant pathotypes. Of the 23 pathogenic E. coli identified from 14 samples based on their gene contents, >95% (n = 22) were resistant to at least one antibiotic and 13% (n = 3) of isolates were resistant to ≥3 classes of antibiotics. Several factors including the time of milking, hygiene practices of the producers, cow breed and amount of milk produced by the cow were found to be significantly associated with high APC of milk samples. In conclusion, both raw and commercially pasteurized milk are highly contaminated with fecal organisms. For intervention, more emphasis should be given at producer's level as microorganisms introduced to milk at this stage get the longest time for survival and multiplication.
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http://dx.doi.org/10.1016/j.ijfoodmicro.2018.04.028DOI Listing
August 2018

Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis.

Sci Rep 2018 03 15;8(1):4628. Epub 2018 Mar 15.

Robert Koch Institute, Berlin, 13353, Germany.

Pyrazinamide (PZA) is an important first-line anti-tuberculosis drug, resistance to which occurs primarily due to mutations in pncA (Rv2043c) that encodes the pyrazinamidase enzyme responsible for conversion of pro-drug PZA into its active form. Previous studies have reported numerous resistance-conferring mutations distributed across the entire length of pncA without any hotspot regions. As different lineages of Mycobacterium tuberculosis display a strong geographic association, we sought to understand whether the genetic background influenced the distribution of mutations in pncA. We analyzed the whole genome sequence data of 1,480 clinical isolates representing four major M. tuberculosis lineages to identify the distribution of mutations in the complete operon (Rv2044c-pncA-Rv2042c) and its upstream promoter region. We observed a non-overlapping pattern of mutations among various lineages and identified a lineage 3-specific frame-shift deletion in gene Rv2044c upstream of pncA that disrupted the stop codon and led to its fusion with pncA. This resulted in the addition of a novel domain of unknown function (DUF2784) to the pyrazinamidase enzyme. The variant molecule was computationally modelled and physico-chemical parameters determined to ascertain stability. Although the functional impact of this mutation remains unknown, its lineage specific nature highlights the importance of genetic background and warrants further study.
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http://dx.doi.org/10.1038/s41598-018-22883-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5854631PMC
March 2018

AmpliSeq Screening of Genes Encoding the C-Type Lectin Receptors and Their Signaling Components Reveals a Common Variant in Associated with Pulmonary Tuberculosis in an Indian Population.

Front Immunol 2018 20;9:242. Epub 2018 Feb 20.

ZIK Septomics, Jena University Hospital, Jena, Germany.

Tuberculosis (TB) is a multifactorial disease governed by bacterial, host and environmental factors. On the host side, growing evidence shows the crucial role that genetic variants play in the susceptibility to (Mtb) infection. Such polymorphisms have been described in genes encoding for different cytokines and pattern recognition receptors (PRR), including numerous Toll-like receptors (TLRs). In recent years, several members of the C-type lectin receptors (CTLRs) have been identified as key PRRs in TB pathogenesis. Nevertheless, studies to date have only addressed particular genetic polymorphisms in these receptors or their related pathways in relation with TB. In the present study, we screened the main CTLR gene clusters as well as CTLR pathway-related genes for genetic variation associated with pulmonary tuberculosis (PTB). This case-control study comprised 144 newly diagnosed pulmonary TB patients and 181 healthy controls recruited at the Bhagwan Mahavir Medical Research Center (BMMRC), Hyderabad, India. A two-stage study was employed in which an explorative AmpliSeq-based screening was followed by a validation phase using iPLEX MassARRAY. Our results revealed one SNP (rs3774275) in significantly associated with PTB in our population (joint analysis  = 0.0028). Furthermore, serum levels of MASP1 were significantly elevated in TB patients when compared to healthy controls. Moreover, in the present study we could observe an impact of increased MASP1 levels on the lectin pathway complement activity . In conclusion, our results demonstrate a significant association of polymorphism rs3774275 and MASP1 serum levels with the development of pulmonary TB. The present work contributes to our understanding of host-Mtb interaction and reinforces the critical significance of mannose-binding lectin and the lectin-complement pathway in Mtb pathogenesis. Moreover, it proposes a polymorphism as a potential genetic marker for TB resistance.
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http://dx.doi.org/10.3389/fimmu.2018.00242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826192PMC
March 2019

Colistin resistant carrying - in urban sludge samples: Dhaka, Bangladesh.

Gut Pathog 2017 20;9:77. Epub 2017 Dec 20.

International Center for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, 1212 Bangladesh.

Of 48 bacteria belonging to the family tested from urban sludge samples, one isolate was resistant to colistin and possessed the resistance marker gene - found for the first time from Bangladesh. The colistin resistant was multidrug resistant showing resistance to 11 different antibiotics tested.
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http://dx.doi.org/10.1186/s13099-017-0227-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738163PMC
December 2017

Risk of Transmission of Antimicrobial Resistant from Commercial Broiler and Free-Range Retail Chicken in India.

Front Microbiol 2017 13;8:2120. Epub 2017 Nov 13.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India.

Multidrug-resistant infections are a growing public health concern. This study analyzed the possibility of contamination of commercial poultry meat (broiler and free-range) with pathogenic and or multi-resistant in retail chain poultry meat markets in India. We analyzed 168 isolates from broiler and free-range retail poultry (meat/ceca) sampled over a wide geographical area, for their antimicrobial sensitivity, phylogenetic groupings, virulence determinants, extended-spectrum-β-lactamase (ESBL) genotypes, fingerprinting by Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR and genetic relatedness to human pathogenic using whole genome sequencing (WGS). The prevalence rates of ESBL producing among broiler chicken were: meat 46%; ceca 40%. Whereas, those for free range chicken were: meat 15%; ceca 30%. from broiler and free-range chicken exhibited varied prevalence rates for multi-drug resistance (meat 68%; ceca 64% and meat 8%; ceca 26%, respectively) and extraintestinal pathogenic (ExPEC) contamination (5 and 0%, respectively). WGS analysis confirmed two globally emergent human pathogenic lineages of , namely the ST131 (30-Rx subclone) and ST117 among our poultry isolates. These results suggest that commercial poultry meat is not only an indirect public health risk by being a possible carrier of non-pathogenic multi-drug resistant (MDR)-, but could as well be the carrier of human pathotypes. Further, the free-range chicken appears to carry low risk of contamination with antimicrobial resistant and extraintestinal pathogenic (ExPEC). Overall, these observations reinforce the understanding that poultry meat in the retail chain could possibly be contaminated by MDR and/or pathogenic
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http://dx.doi.org/10.3389/fmicb.2017.02120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694193PMC
November 2017

Existence of a novel variant in quinolone resistant from aquatic habitats of Bangladesh.

Gut Pathog 2017 23;9:58. Epub 2017 Oct 23.

International Center for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, 1212 Bangladesh.

Of 19 environmental (n = 12) and (n = 7) tested for quinolone resistance-related genes , , , and , four each of and possessed , and another isolate possessed a new variant of . This is the first detection of in environmentally dwelling bacteria in Bangladesh.
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http://dx.doi.org/10.1186/s13099-017-0207-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654019PMC
October 2017

Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic (ExPEC) Lineages.

mBio 2017 10 24;8(5). Epub 2017 Oct 24.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, India

sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producing clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 strains with 40 genomes from three other STs, including ST38 ( 12), ST405 ( 10), and ST648 ( 18), and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases) has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage., particularly the ST131 extraintestinal pathogenic (ExPEC) lineage, is an important cause of community- and hospital-acquired infections, such as urinary tract infections, surgical site infections, bloodstream infections, and sepsis. The treatment of infections caused by ExPEC has become very challenging due to the emergence of resistance to the first-line as well as the last-resort antibiotics. This study analyzes ST131 against three other important and globally distributed ExPEC lineages (ST38, ST405, and ST648) that also produced extended-spectrum β-lactamase (ESBL). This is perhaps the first study that employs the high-throughput whole-genome sequence-based approach to compare and study the genomic features of these four ExPEC lineages in relation to their functional properties. Findings from this study highlight the differences in the genomic coordinates of ST131 with respect to the other STs considered here. Results from this comparative genomics study can help in advancing the understanding of ST131 evolution and also offer a framework towards future developments in pathogen identification and targeted therapeutics to prevent diseases caused by this pandemic ST131 clone.
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http://dx.doi.org/10.1128/mBio.01596-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654935PMC
October 2017

Comparative Genomics of Isolated from Skin and Soft Tissue and Other Extraintestinal Infections.

mBio 2017 08 15;8(4). Epub 2017 Aug 15.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, India

, an intestinal Gram-negative bacterium, has been shown to be associated with a variety of diseases in addition to intestinal infections, such as urinary tract infections (UTIs), meningitis in neonates, septicemia, skin and soft tissue infections (SSTIs), and colisepticemia. Thus, for nonintestinal infections, it is categorized as extraintestinal pathogenic (ExPEC). It is also an opportunistic pathogen, causing cross infections, notably as an agent of zoonotic diseases. However, comparative genomic data providing functional and genetic coordinates for ExPEC strains associated with these different types of infections have not proven conclusive. In the study reported here, ExPEC isolated from SSTIs was characterized, including virulence and drug resistance profiles, and compared with isolates from patients suffering either pyelonephritis or septicemia. Results revealed that the majority of the isolates belonged to two pathogenic phylogroups, B2 and D. Approximately 67% of the isolates were multidrug resistant (MDR), with 85% producing extended-spectrum beta-lactamase (ESBL) and 6% producing metallo-beta-lactamase (MBL). The genotype was observed in at least 70% of the isolates in each category, conferring resistance to an extended range of beta-lactam antibiotics. Whole-genome sequencing and comparative genomics of the ExPEC isolates revealed that two of the four isolates from SSTIs, NA633 and NA643, belong to pandemic sequence type ST131, whereas functional characteristics of three of the ExPEC pathotypes revealed that they had equal capabilities to form biofilm and were resistant to human serum. Overall, the isolates from a variety of ExPEC infections demonstrated similar resistomes and virulomes and did not display any disease-specific functional or genetic coordinates. Infections caused by extraintestinal pathogenic (ExPEC) are of global concern as they result in significant costs to health care facilities management. The recent emergence of a multidrug-resistant pandemic clone, ST131, is of primary concern as a global threat. In developing countries, such as India, skin and soft tissue infections (SSTIs) associated with are marginally addressed. In this study, we employed both genomic analysis and phenotypic assays to determine relationships, if any, among the ExPEC pathotypes. Similarity between antibiotic resistance and virulence profiles was observed, ST131 isolates from SSTIs were reported, and genomic similarities among strains isolated from different disease conditions were detected. This study provides functional molecular infection epidemiology insight into SSTI-associated compared with ExPEC pathotypes.
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http://dx.doi.org/10.1128/mBio.01070-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559633PMC
August 2017

DosR Regulon Gene Encodes a Novel Antigen with Pro-inflammatory Functions and Potential Diagnostic Application for Detection of Latent Tuberculosis.

Front Immunol 2017 24;8:712. Epub 2017 Jun 24.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India.

Approximately 1.7 billion people in the world harbor latent (Mtb) with a substantial risk of progression to clinical outcome. Containment of these seed beds of Mtb is essential to eliminate tuberculosis completely in high burden settings such as India. Hence, there is an urgent need for the identification of new serological markers for detection or vaccine candidates to prevent latent tuberculosis infection (LTBI). DosR regulon antigens of Mtb might serve as attractive targets for LTBI diagnosis or vaccine development as they are specifically expressed and are upregulated during latent phase. In this study, we investigated the role of , a member of DosR regulon (exclusive to Mtb complex), in host-pathogen interaction and its immunogenic potential in LTBI, active TB, and healthy control cohorts. Rv2004c elicited strong antibody response in individuals with LTBI compared to active TB patients and healthy cohorts. Recombinant Rv2004c induced pro-inflammatory cytokine response in human peripheral blood mononuclear cells and THP-1 cells NF-κB phosphorylation. Interaction of Rv2004c with toll-like receptor (TLR)-2 was confirmed using HEK-Blue hTLR-2 and pull-down assays. Rv2004c enhanced the surface expression of TLR-2 at mRNA and protein levels in THP-1 cells. Our findings revealed that Rv2004c induces strong humoral and cell mediated immune responses. Given these observations, we propose Rv2004c to be a potential diagnostic marker or an attractive vaccine candidate that can be useful against LTBI.
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http://dx.doi.org/10.3389/fimmu.2017.00712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483032PMC
June 2017