Nosocomial transmission of Shigella dysenteriae type 1

Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage

Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.

Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa

Background

In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections.

Objectives

To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region.

Methods

A PubMed database literature search (English language only) was performed using the search strings: ‘Africa outbreak MDR’, ‘Africa outbreak multi’, ‘Africa outbreak multidrug’, ‘Africa outbreak multi drug’, ‘Africa outbreak resistance’, ‘Africa outbreak resistant’, ‘Africa outbreak drug’, ‘Africa outbreak antibiotic’, ‘Africa outbreak antimicrobial’. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review.

Results

The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used.

Conclusion

Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies.

Hospital Wastewater Releases of Carbapenem-Resistance Pathogens and Genes in Urban India

Increasing antibiotic resistant hospital-acquired infections and limited new antibiotic discovery are jeopardizing human health at global scales, although how hospitals themselves fuel antimicrobial resistance (AMR) in the wider environment is largely unknown. Antibiotic resistance (AR) in hospitals in countries such as India is potentially problematic because of high antibiotic use, overcrowding, and inadequate wastewater containment. Here we quantified fecal coliforms (FC), carbapenem-resistant Enterobacteriaceae (CRE), bla_NDM-1, and selected extended-spectrum β-lactam (ESBL) resistant bacteria and genes in 12 hospital wastewater outfalls and five background sewer drains across New Delhi over two seasons. Hospital wastewaters had up to 9 orders of magnitude greater concentrations of CRE bacteria and bla_NDM-1 than local sewers (depending on the hospital), implying hospitals contribute high concentrations of AR relative to community sources in Delhi, especially during the winter. Significant correlations were found between FC levels (a fecal indictor), and CRE (r = 0.924; p = 0.005), bla_NDM-1 (r = 0.934, p = 0.009), and ESBL-resistant bacteria (r = 0.913, p = 0.010) levels across hospital wastewaters, respectively, implying that elevated CRE and bla_NDM-1 are of patient origin. However, of greater importance to global health, microbial culturing found 18 to 41% of wastewater CRE isolates (n = 1447) were on the WHO "critical pathogen" list in urgent need of new antibiotics, and 55% of CRE isolates from larger hospitals carried at least one bla_NDM-1 gene. Wastewater releases from New Delhi hospitals may pose a greater AR exposure risk to residents than believed, implying in-hospital antibiotic use must be better controlled and more effective waste treatment is needed for hospital wastewaters.

Transmission and strain variation of Shigella flexneri 4a after mass prophylaxis in a long-stay psychiatric centre

Shigella flexneri 4a caused sustained outbreaks in a large long-stay psychiatric centre, Taiwan, 2001-2006. Trimethoprim-sulphamethoxazole (SXT) prophylaxis was administered in 2004. We recovered 108 S. flexneri 4a isolates from 83 symptomatic (including one caregiver) and 12 asymptomatic subjects (11 contacts, one caregiver). The isolates were classified into eight antibiogram types and 15 genotypes (six clusters) by using antimicrobial susceptibility testing and pulsed-field gel electrophoresis of NotI-digested DNA, respectively. These characteristics altered significantly after SXT prophylaxis (P < 0·05), with concomitant emergence of SXT-resistant isolates in two antibiogram types. P01 (n = 71), the predominant epidemic genotype, caused infection in two caregivers and five patients under their care; two P01 isolates were recovered from the same patient 6 months apart. These results indicate the importance of sustained person-to-person transmission of S. flexneri 4a by long-term convalescent, asymptomatic or caregiver carriers, and support the emergence of SXT-resistant strains following selective pressure by SXT prophylaxis.

Part II. Analysis of data gaps pertaining to Shigella infections in low and medium human development index countries, 1984-2005

The global incidence of Shigella infection has been estimated at 80-165 million episodes annually, with 99% of episodes occurring in the developing world. To identify contemporary gaps in the understanding of the global epidemiology of shigellosis, we conducted a review of the English-language scientific literature from 1984 to 2005, restricting the search to low and medium human development countries. Our review yielded 11 population-based studies of Shigella burden from seven countries. No population-based studies have been conducted in sub-Saharan Africa or in low human development countries. In studies done in all age groups, Shigella incidence varied from 0.6 to 107 episodes/1000 person-years. S. flexneri was the most commonly detected subgroup in the majority of studies. Case-fatality rates ranged from 0% to 2.6% in population-based studies and from 0% to 21% in facility-based studies. This review highlights the large gaps in data on the burden of Shigella infections for low human development index countries and, more specifically, for sub-Saharan Africa.

Nosocomial diarrhoea

Toroviruses have been reported as a new cause of nosocomial viral diarrhoea, and the role of astroviruses has been further elucidated. Polymerase chain reaction methods promise to improve the diagnosis and understanding of the aetiology and control of hospital-acquired viral gastroenteritis. A clearer picture of the impact and extent of Clostridium difficile diarrhoea has emerged, and several control measures have been described. An epidemic Clostridium difficile strain and toxin A-deficient strains have been reported. There is growing evidence that enterotoxin-producing Clostridium perfringens can also cause antibiotic-associated diarrhoea.

Antimicrobial resistance in developing countries. Part I: recent trends and current status

The global problem of antimicrobial resistance is particularly pressing in developing countries, where the infectious disease burden is high and cost constraints prevent the widespread application of newer, more expensive agents. Gastrointestinal, respiratory, sexually transmitted, and nosocomial infections are leading causes of disease and death in the developing world, and management of all these conditions has been critically compromised by the appearance and rapid spread of resistance. In this first part of the review, we have summarised the present state of resistance in these infections from the available data. Even though surveillance of resistance in many developing countries is suboptimal, the general picture is one of accelerating rates of resistance spurred by antimicrobial misuse and shortfalls in infection control and public health. Reservoirs for resistance may be present in healthy human and animal populations. Considerable economic and health burdens emanate from bacterial resistance, and research is needed to accurately quantify the problem and propose and evaluate practicable solutions. In part II, to be published next month, we will review potential containment strategies that could address this burgeoning problem.