Whole genomes from bacteria collected at diagnostic units around the world 2020

The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.

Prevalence of extended spectrum Beta-Lactamase producing Klebsiella species from patients’ specimens in a tertiary teaching hospital in Ile-Ife, Southwest Nigeria

Objective: This study determined the prevalence of ESBL genes amongst Klebsiella species isolated from patients’ specimens attending a Tertiary Teaching Hospital, in Ile-Ife, Southwest Nigeria. Methods: A cross sectional study of presumptive isolates of Klebsiella (n=180) were collected, after ethical approval in the microbiology laboratory. Isolates were identified to species level by conventional biochemical tests and MicrobactTM 24E Identification Kits. Antibiotic susceptibility testing was performed by the Kirby Bauer’s disk diffusion method. ESBL production was detected by the double disc synergy and ESBL genes by the multiplex PCR protocol. Results: The Klebsiella species identified were Klebsiella pneumoniae 95.6%, Klebsiella oxytoca 3.3%, Klebsiella ornithinolytica 0.6% and Klebsiella terrigena 0.6%. The prevalence of ESBL genes among the Klebsiella isolates was 47.2% , and the most common ESBL gene was blaSHV (38.9%), also 75% of the study isolates had MAR index greater than 0.2. Conclusions: The study establishes the prevalence of Extended Spectrum Beta-Lactamase producing Klebsiella sp in the hospital and identified the most prevalent ESBL genes circulating as blaSHV followed by blaTEM and blaCTX-M in this environment. This underscores the need for regular and continuous surveillance of antimicrobial resistance trend as a strong component of the antibiotics stewardship and infection prevention and control programs in the hospital. Keywords: Antibiotic Resistance; Klebsiella; ESBL.

Detection of NDM-1 in Metallo-Beta-Lactamase-Producing Strains of Pseudomonas aeruginosa isolates from a Tertiary Hospital in Southwest Nigeria

BACKGROUND

Metallo-beta-lactamase producingPseudomonas aeruginosa (MBL-PA) infections pose a major healthcare concern globally due to the associated extended morbidity, increased cost of treatment and high mortality.

OBJECTIVES

This study aimed to determine the prevalence of circulating MBL-PA strains and evaluate probable risk factors associated with the carriage of MBL-PA among patients in a selected South-western tertiary hospital in Nigeria.

METHODS

One hundred and forty-four isolates recovered from diverse clinical specimens were identified as Pseudomonas aeruginosa by conventional methods. Eight antibiotics were tested on the isolates using Kirby-Bauer disc diffusion technique. All carbapenem resistant isolates were phenotypically screened for MBL-production using the combined disc synergy test. The MBL-producing strains were evaluated for the presence of three MBL genes blaIMP, blaVIM-2 and blaNDM1 by Polymerase chain reaction (PCR).

RESULTS

Fourteen (9.7%) isolates were positive for metallobeta-lactamase production by combined disc synergy test. The MBL-producing strains were more commonly resistant to all the tested antibiotics except to piperacillin tazobactam and imipenem compared with the non MBL producing strains (p<0.05). Antibiotic use and the occurrence of multidrug resistance phenotype were significantly associated with MBLcarriage (p<0.05). Four (28.6%) MBL-PA isolates carried NDM-1 gene, while IMP and VIM-2 genes were not detected in any of the isolates.

CONCLUSION

The study demonstrated a low prevalence of NDM-1 in P. aeruginosa circulating among patients in this environment. This may be because carbapenems are seldom prescribed in our hospital or probably due to the existence of other MBL genes and non-enzymatic resistance mechanisms that we did not investigate. Studies that evaluate the level of carbapenem resistance via non-MBL production route could assist and improve future surveillance of these fast spreading genes.

Antibiotic resistance pattern of Pseudomonas spp. from patients in a tertiary hospital in South-West Nigeria

Introduction

Pseudomonads constitute critical agents of opportunistic infections in hospital settings particularly in immunocompromised patients and Pseudomonas aeruginosa is a major flagship member of these infectious agents. This study assessed the distribution of Pseudomonas spp. associated with infections in patients and their antibiotic resistance patterns as part of an antibiotic stewardship intervention program and resistance surveillance.

Methods

One hundred and fifty Pseudomonas spp. from different clinical specimens were obtained from the Obafemi Awolowo University Teaching Hospitals Complex Ile-Ife. Culture was carried out on MacConkey and blood agar while phenotypic characterization was done by Gram staining, oxidase, and catalase test. Species identification was done using MICROBACT^TM 24E bacterial identification kit and confirmed by 16S rDNA polymerase chain reaction (PCR) assay. Antibiotic susceptibility testing to eight antibiotics in four classes was done.

Results

Pseudomonas aeruginosa was the most frequently occurring species (96.0%); P. putida (2.67%) and P. fluorescens (0.67%) were also identified as well as an isolate of Burkholderia pseudomallei (0.67%). The highest resistance rate among isolates was observed towards gentamicin (35.4%); piperacillin/tazobactam was the most active antibiotic. Multidrug-resistant (MDR) strains constituted 12.8% of the isolates and most MDR strains also displayed a high multiple antibiotic resistance index (MAR).

Conclusions

Pseudomonas aeruginosa is emerging as a highly MDR pathogen in our hospital setting. This calls for the establishment of a surveillance system and antimicrobial stewardship programme in place. Furthermore, we propose a review of the current antibiotics prescription policy, and infection control programmes (ICPs) if we must control the spread of MDR-P. aeruginosa in this environment.

Clinical presentation and outcome of tuberculosis patients infected by M. africanum versus M. tuberculosis

SETTING

A tuberculosis (TB) case contact study in the Gambia.

OBJECTIVE

To test whether Mycobacterium africanum, which has lost around 68 kb compared with M. tuberculosis sensu stricto, causes less severe TB disease.

DESIGN

We genotyped mycobacterial isolates and compared clinical and radiological characteristics as well as outcome data of M. africanum-infected TB patients with those infected with M. tuberculosis.

RESULTS

Of 317 index cases, 301 had a mycobacterial isolate available, 290 of which had an interpretable spoligotype pattern. Of these, 110 isolates (38%) were M. africanum and 180 (62%) were M. tuberculosis. M. africanum cases had lower body mass indices (17 vs. 17.45 for M. tuberculosis-infected patients, P = 0.029) and their radiographic disease was more extensive (96% vs. 89% had at least moderately severe radiographic changes, P = 0.031). Outcome on treatment was similar (2.8% of human immunodeficiency virus [HIV] negative M. africanum patients died on treatment vs. 3.0% of M. tuberculosis patients, P = 0.95).

CONCLUSION

M. africanum causes sputum smear-positive tuberculosis disease that is at least as severe as that caused by M. tuberculosis sensu stricto. Further clinical comparisons may be helpful in smear-negative patients and HIV-TB co-infected patients, and to identify whether there is any difference in time to develop disease.

Does resistance to pyrazinamide accurately indicate the presence of Mycobacterium bovis?

Mycobacterium bovis is best identified by screening those isolates of the Mycobacterium tuberculosis complex that have any pyrazinamide (PZA) resistance, using a confirmatory test such as spoligotyping, biochemical testing, or genomic deletion analysis. The sensitivity for detection of M. bovis is lowered to 82% when only PZA-monoresistant isolates are screened.

Genomic analysis distinguishes Mycobacterium africanum

Mycobacterium africanum is thought to comprise a unique species within the Mycobacterium tuberculosis complex. M. africanum has traditionally been identified by phenotypic criteria, occupying an intermediate position between M. tuberculosis and M. bovis according to biochemical characteristics. Although M. africanum isolates present near-identical sequence homology to other species of the M. tuberculosis complex, several studies have uncovered large genomic regions variably deleted from certain M. africanum isolates. To further investigate the genomic characteristics of organisms characterized as M. africanum, the DNA content of 12 isolates was interrogated by using Affymetrix GeneChip. Analysis revealed genomic regions of M. tuberculosis deleted from all isolates of putative diagnostic and biological consequence. The distribution of deleted sequences suggests that M. africanum subtype II isolates are situated among strains of "modern" M. tuberculosis. In contrast, other M. africanum isolates (subtype I) constitute two distinct evolutionary branches within the M. tuberculosis complex. To test for an association between deleted sequences and biochemical attributes used for speciation, a phenotypically diverse panel of "M. africanum-like" isolates from Guinea-Bissau was tested for these deletions. These isolates clustered together within one of the M. africanum subtype I branches, irrespective of phenotype. These results indicate that convergent biochemical profiles can be independently obtained for M. tuberculosis complex members, challenging the traditional approach to M. tuberculosis complex speciation. Furthermore, the genomic results suggest a rational framework for defining M. africanum and provide tools to accurately assess its prevalence in clinical specimens.