Naveen Kumar Devanga Ragupathi

Draft Genome Sequences of Three Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Isolates from Bacteremia

ABSTRACT Hypervirulent Klebsiella pneumoniae strains have been increasingly reported worldwide, and there is emergence of carbapenem resistance among them. Here, we report the genome sequences of three carbapenem-resistant hypervirulent K. pneumoniae isolates isolated from bacteremic patients at a tertiary-care center in South India.

Draft genome sequence of blaTEM-1-mediated cephalosporin-resistant Salmonella enterica serovar Typhi from bloodstream infection

Enteric fever is a major cause of concern in developing countries across the globe. The primary choice of antibiotics remains fluoroquinolones, followed by cephalosporins. Resistance to third-generation cephalosporins is rarely reported in Salmonella enterica serovar Typhi. This study reports the whole genome sequence of an S. Typhi isolate resistant to cefixime [minimum inhibitory concentration (MIC)=512μg/mL] by microbroth dilution. Interestingly, the isolate was negative for the cephalosporin resistance gene blaCTX-M by PCR, which is a known mechanism for higher cephalosporin resistance. The isolate was further subjected to next-generation sequencing that identified blaTEM-1B and blaDHA-1 genes in association with qnrB4 and sul1. blaTEM is a known gene coding for β-lactam resistance. In certain cases, overexpression of blaTEM was reported to result in cephalosporin resistance. This suggests that the high cefixime MIC would have been contributed by overexpression of blaTEM-1B. The blaTEM-1B gene was found to be associated with a promoter Px with -35 and -10 regions as TTAATA and TAAAGT, respectively. The promoter regions were unique, but the -10 region was similar to that found in Pa/Pb (previously reported promoter for blaTEM) with a single nucleotide change. In addition, an IncN plasmid was identified, which is usually reported in association with the most prevalent extended-spectrum β-lactamase (ESBL), metallo- and non-metallo-carbapenemase, and plasmid-mediated quinolone resistance (PMQR) genes. Plasmids such as IncN might possibly confer resistance and enhance spread. It is imperative to continuously monitor the drug resistance profile and evolving genetic elements.

Whole-Genome Shotgun Sequencing of Cephalosporin-Resistant Salmonella enterica Serovar Typhi

ABSTRACT Typhoid is one of the leading causes of mortality in developing countries. Here, we report the draft genome sequences of four Salmonella enterica serovar Typhi strains isolated from bloodstream infections in a tertiary care hospital. The sequence data indicate genomes of ~4.5 Mb for all isolates, with one plasmid in each.

Molecular Characterization of Intermediate Susceptible Typhoidal Salmonella to Ciprofloxacin, and its Impact

Background and ObjectiveExtensive use of ciprofloxacin to treat Salmonella typhi infections has led to the emergence of resistance, resulting in clinical failure and delayed treatment response. Interpretative breakpoints for ciprofloxacin were revised by the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) in 2012. Since the majority of S. typhi isolates fall under the category of ‘intermediate susceptible’ as per CLSI criteria, we undertook molecular characterization to better define the susceptibility of these isolates.MethodsOf 113 typhoidal Salmonella isolates collected during 2014, 33 (27 S. typhi and 6 S. paratyphi A) were randomly selected to determine the presence of chromosomal (gyrA, gyrB and parC), plasmid (qnrA, qnrB, qnrS and aac(6′)-lb-cr), and efflux-mediated fluoroquinolone resistance.ResultsTo the best of our knowledge, the parC mutation Glu(84)-Gly was observed for the first time in S. typhi in India. Of 33 isolates, only one harbored the qnrB gene, which is responsible for plasmid-mediated resistance. No significant change in efflux pump activity was observed for ciprofloxacin, except one that showed a fivefold decrease. Ninety-six percent of isolates with intermediate minimum inhibitory concentration to ciprofloxacin (CLSI) had mutations in the gyrA and parC genes, which might translate to possible/probable clinical failure in patients if treated with ciprofloxacin. In contrast, the EUCAST criteria define these isolates as resistant and may result in appropriate therapy with reduced morbidity.ConclusionIt was clear that the molecular mechanism of ciprofloxacin resistance correlates better with the EUCAST criteria than the CLSI criteria, which is also in agreement with the pefloxacin results, suggesting it as a surrogate marker for identifying fluoroquinolone susceptibility.

First Report on the Draft Genome Sequences of Corynebacterium diphtheriae Isolates from India.

ABSTRACT We report here the draft genome sequences of five Corynebacterium diphtheriae isolates of Indian origin. The C. diphtheriae isolates TH1141, TH510, TH1526, TH1337, and TH2031 belong to sequence type ST-50, ST-295, ST-377, ST-405, and ST-405, with an average genome size of 2.5 Mbp.

Draft Genome Sequence of an Extended-Spectrum-β-Lactamase-Positive Hypervirulent Klebsiella pneumoniae Strain with Novel Sequence Type 2318 Isolated from a Neonate

ABSTRACT Antimicrobial resistance among hypervirulent Klebsiella pneumoniae is increasingly reported. Here, we report the draft genome sequence of a hypervirulent K. pneumoniae strain isolated from a neonate with sepsis belonging to novel sequence type 2318 (ST2318).

Whole genome analysis of hypervirulent Klebsiella pneumoniae isolates from community and hospital acquired bloodstream infection

BackgroundHypervirulent K. pneumoniae (hvKp) causes severe community acquired infections, predominantly in Asia. Though initially isolated from liver abscesses, they are now prevalent among invasive infections such as bacteraemia. There have been no studies reported till date on the prevalence and characterisation of hvKp in India. The objective of this study is to characterise the hypervirulent strains isolated from bacteraemic patients for determination of various virulence genes and resistance genes and also to investigate the difference between healthcare associated and community acquired hvKp with respect to clinical profile, antibiogram, clinical outcome and molecular epidemiology.ResultsSeven isolates that were susceptible to all of the first and second line antimicrobials and phenotypically identified by positive string test were included in the study. They were then confirmed genotypically by presence of rmpA and rmpA2 by PCR. Among the study isolates, four were from patients with healthcare associated infections; none were fatal. All patients with community acquired infection possessed chronic liver disease with fatal outcome. Genes encoding for siderophores such as aerobactin, enterobactin, yersiniabactin, allantoin metabolism and iron uptake were identified by whole genome sequencing. Five isolates belonged to K1 capsular type including one K. quasipneumoniae. None belonged to K2 capsular type. Four isolates belonged to the international clone ST23 among which three were health-care associated and possessed increased virulence genes. Two novel sequence types were identified in the study; K. pneumoniae belonging to ST2319 and K. quasipneumoniae belonging to ST2320. Seventh isolate belonged to ST420.ConclusionThis is the first report on whole genome analysis of hypervirulent K. pneumoniae from India. The novel sequence types described in this study indicate that these strains are evolving and hvKp is now spread across various clonal types. Studies to monitor the prevalence of hvKp is needed since there is a potential for the community acquired isolates to develop multidrug resistance in hospital environment and may pose a major challenge for clinical management.

Draft Genome Sequence of Extremely Drug-Resistant Pseudomonas aeruginosa (ST357) Strain CMC_VB_PA_B22862 Isolated from a Community-Acquired Bloodstream Infection

ABSTRACT Extremely drug-resistant Pseudomonas aeruginosa strains causing severe infections have become a serious concern across the world. Here, we report draft genome sequence of P. aeruginosa with an extremely drug-resistant profile isolated from a patient with community-acquired bloodstream infection in India.

First report of blaOXA-181-mediated carbapenem resistance in Aeromonas caviae in association with pKP3-A: Threat for rapid dissemination

OBJECTIVES Carbapenemase-producing Aeromonas spp. are of great concern in healthcare settings and are also known to acquire clinically relevant resistance genes. In this study, carbapenem-non-susceptible Aeromonas isolates were characterised for their molecular mechanisms of resistance. METHODS Among 180 Aeromonas isolates, 10 carbapenem-non-susceptible isolates were selected based on their antimicrobial susceptibility profile. Carbapenemase production was investigated by the CarbaNP test. ESBL-, AmpC- and carbapenemase-encoding genes were screened by PCR. Isolates VBF557 and VBF856 with high MICs for imipenem were selected for whole-genome sequencing (WGS). Conjugation experiments were performed to determine the transmissibility of resistance. RESULTS WGS remarkably revealed the presence of class D β-lactamases (AmpS/AmpH), class C β-lactamases and class B2 metallo-β-lactamase (cphA3) in VBF557. In contrast, VBF856 had multiple resistance genes coding for aminoglycoside, sulphonamide, carbapenem (blaOXA-181 class D β-lactamase), macrolide, fluoroquinolone, rifampicin, phenicol, tetracycline and trimethoprim resistance. This is the first global report of blaOXA-181 in Aeromonas spp. Interestingly, blaOXA-181 was identified in association with transposon Tn2013 in plasmid pKP3-A. Additionally, an IncQ2 plasmid with qnrS2 was identified. Among the tested isolates, VBF1116 and VBF888 possessed blaNDM and blaVEB, respectively, by PCR. None of the other isolates harboured any tested β-lactamase genes. The resistance gene was transmissible in the presence of imipenem. CONCLUSIONS Presence of such resistance genes in plasmids further adds complexity for control of spread of carbapenem resistance. This study reveals the emergence of carbapenem resistance among Aeromonas spp. and the importance of mobile genetic elements such as plasmids in interchanging resistance determinants between species.

Molecular diagnosis of non-serotypeable Shigella spp.: Problems and Prospects

It is not always possible to identify Shigella serogroups/serotypes by biochemical properties alone. Specific identification requires serotyping. Occasionally, isolates that resemble Shigella spp. biochemically, but are non-agglutinable with available antisera, have been observed. Several mechanisms have been reported to limit the efficiency of the serotyping assay. Serotype conversion is a major mechanism in Shigella spp. to escape protective host immune responses. This easy conversion through significant modification of the O-antigen backbone results in different serotypes, which makes laboratory identification difficult. Furthermore, members of the family Enterobacteriaceae are closely related and there is antigenic cross-over (intra- and inter-specific cross-reaction) which affects the agglutination reaction. The performance of the available methods for identification of non-serotypeable Shigella is discussed here, and reveals them to be non-reliable. This shows a need for an alternative method for identification and typing of Shigella spp.