Genome Sequences of Five Novel Neisseria gonorrhoeae Sequence Types Isolated in KwaZulu-Natal, South Africa

ABSTRACT Africa has the highest incidence of Neisseria gonorrhoeae infections globally, but data on these isolates is scarce. Here, we report six N. gonorrhoeae genome sequences with five novel sequence types isolated from patients with uncomplicated genitourinary gonorrhea in South Africa.

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Antimicrobial resistance mechanisms, MLST and NG-STAR sequence types of diverse Neisseria gonorrhoeae isolates in KwaZulu-Natal, South Africa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00759-21 ◽

2021 ◽

Author(s):

Nireshni Mitchev ◽

Ravesh Singh ◽

Mushal Allam ◽

Stanford Kwenda ◽

Arshad Ismail ◽

...

Keyword(s):

South Africa ◽

Antimicrobial Resistance ◽

Neisseria Gonorrhoeae ◽

Point Mutations ◽

Resistance Mechanisms ◽

Public Healthcare ◽

Multiple Sequence ◽

Genotypic Analysis ◽

Kwazulu Natal ◽

Sequence Types

Objective: Antimicrobial resistance (AMR) is a major challenge to managing infectious diseases. Africa has the highest incidence of gonorrhoea but there is a lack of comprehensive data from sparse surveillance programs. This study investigated the molecular epidemiology and AMR profiles of Neisseria gonorrhoeae isolates in KwaZulu-Natal province (KZN), South Africa. Methods: Repository isolates, from patients attending public healthcare clinics for STI care, were used for phenotypic and genotypic analysis. Etest® was performed to determine antimicrobial susceptibility. Whole-genome sequencing (WGS) was used to determine epidemiology and to predict susceptibility by detecting resistance-associated genes and mutations. Results: Among the 61 isolates, multiple sequence types were identified. Six isolates were novel as determined by multilocus sequence typing. N.gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) determined 48 sequence types, of which 35 isolates had novel antimicrobial profiles. Two novel penA alleles and eight novel mtrR alleles were identified. Point mutations were detected in gyrA , parC , mtrR , penA , ponA and porB1 . This study revealed a high prevalence of AMR (penicillin 67%, tetracycline 89% and ciprofloxacin 52%). However, spectinomycin, cefixime, ceftriaxone and azithromycin remained 100% effective. Conclusion: This study is one of the first to comprehensively describe the epidemiology and AMR of N. gonorrhoeae in KZN, South Africa and Africa, using WGS. KZN has a wide strain diversity and most of these sequence types have been detected in multiple countries, however more than half of our isolates have novel antimicrobial profiles. Continued surveillance is crucial to monitor the emergence of resistance to cefixime, ceftriaxone and azithromycin.

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Clinical Evaluation of the OneStep Gonorrhea RapiCard InstaTest for Detection of Neisseria gonorrhoeae in Symptomatic Patients from KwaZulu-Natal, South Africa: TABLE 1

Journal of Clinical Microbiology ◽

10.1128/jcm.03603-14 ◽

2015 ◽

Vol 53 (4) ◽

pp. 1348-1350 ◽

Cited By ~ 5

Author(s):

N. S. Abbai ◽

P. Moodley ◽

T. Reddy ◽

T. G. Zondi ◽

S. Rambaran ◽

...

Keyword(s):

South Africa ◽

Neisseria Gonorrhoeae ◽

Screening Tool ◽

Point Of Care ◽

Health Clinic ◽

Content Type ◽

Point Of Care Test ◽

Kwazulu Natal ◽

Low Sensitivity ◽

Public Health Clinic

We evaluated a point-of-care test for the detection ofNeisseria gonorrhoeaein patients attending a public health clinic in KwaZulu-Natal, South Africa. The test showed a low sensitivity against PCR and culture (<40%); however, a higher specificity was observed (>95%). This test is unsuitable as a screening tool for gonorrhea.

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Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

Journal of Clinical Microbiology ◽

10.1128/jcm.02589-14 ◽

2014 ◽

Vol 53 (1) ◽

pp. 191-200 ◽

Cited By ~ 78

Author(s):

Walter Demczuk ◽

Tarah Lynch ◽

Irene Martin ◽

Gary Van Domselaar ◽

Morag Graham ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Large Scale ◽

Epidemiological Studies ◽

23S Rrna ◽

Genome Comparison ◽

Whole Genome ◽

Content Type ◽

Genomic Epidemiology ◽

High Level ◽

Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

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Protected areas and environmental conservation in KwaZulu-Natal, South Africa: on HEIs, livelihoods and sustainable development

International Journal of Sustainability in Higher Education ◽

10.1108/ijshe-05-2020-0157 ◽

2021 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Inocent Moyo ◽

Hlengiwe Marvelous Sweetness Cele

Keyword(s):

South Africa ◽

Sustainable Development ◽

Rural Communities ◽

Indigenous Communities ◽

Environmental Conservation ◽

Developmental Needs ◽

Content Type ◽

Research And Innovation ◽

Kwazulu Natal ◽

Micro Level

Purpose The paper aims to advocate for innovative approaches in terms of the involvement of higher education institutions (HEIs) in the conservation of the environment, which fully considers and includes the developmental needs of indigenous communities while at the same time protecting the environment. Design/methodology/approach Using a qualitative study of indigenous communities and protected area (PA) authorities in Okhahlamba-Drakensberg, KwaZulu-Natal, South Africa, this paper explores the potential of the engagement of HEIs in capacitating indigenous communities to unleash their development potential towards reducing poverty and, thus accelerating the implementation of sustainable development goal one (SDG 1). Findings The paper shows that the enforcement of stringently protectionist policies in environmental conservation in PAs does very little to address issues of poverty because it leads to the marginalisation of indigenous communities and thereby their exclusion from using resources, which should benefit them. This undermines sustainable development, particularly the attainment of SDGs such as Goal 1, which targets ending poverty in all its forms everywhere. Originality/value Using the case of environmental management and governance of a PA in KwaZulu-Natal, South Africa, this paper highlights the fact that the attainment of SDG 1 can start at a micro-level and HEIs have a role to play in terms of collaborating with and understanding the needs of the rural communities so that research and innovation are geared towards meeting such needs. In this way, the paper advances the case of how the HEI-rural community-SDG 1 nexus can be established.

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Draft Genome Sequences of Potentially Pathogenic Clostridium perfringens Strains from Environmental Surface Water in the North West Province of South Africa

Microbiology Resource Announcements ◽

10.1128/mra.00407-19 ◽

2019 ◽

Vol 8 (32) ◽

Cited By ~ 2

Author(s):

Johannes Cornelius Jacobus Fourie ◽

Tomasz J. Sanko ◽

Cornelius Carlos Bezuidenhout ◽

Charlotte Mienie ◽

Rasheed Adegbola Adeleke

Keyword(s):

South Africa ◽

Surface Water ◽

Clostridium Perfringens ◽

Draft Genome ◽

Anthropogenic Factors ◽

Genome Sequences ◽

Content Type ◽

North West ◽

The North ◽

North West Province

Surface water systems in South Africa are experiencing a major decline in quality due to various anthropogenic factors. This poses a possible health risk for humans. Here, we present the draft genome sequences of three Clostridium perfringens isolates obtained from a fecally polluted river system in the North West province of South Africa.

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Resistance Profile of Neisseria gonorrhoeae in KwaZulu-Natal, South Africa Questioning the Effect of the Currently Advocated Dual Therapy

Sexually Transmitted Diseases ◽

10.1097/olq.0000000000000961 ◽

2019 ◽

Vol 46 (4) ◽

pp. 266-270 ◽

Cited By ~ 4

Author(s):

Santhuri Rambaran ◽

Kavitha Naidoo ◽

Navisha Dookie ◽

Prashini Moodley ◽

Adriaan Willem Sturm

Keyword(s):

South Africa ◽

Neisseria Gonorrhoeae ◽

Dual Therapy ◽

Resistance Profile ◽

Kwazulu Natal

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A Culture Collection of 50 Neisseria gonorrhoeae Isolates

Microbiology Resource Announcements ◽

10.1128/mra.00699-20 ◽

2020 ◽

Vol 9 (40) ◽

Author(s):

H. Liu ◽

E. Vidyaprakash ◽

M. W. Schmerer ◽

D. C. Pham ◽

S. St Cyr ◽

...

Keyword(s):

Antibiotic Resistance ◽

Neisseria Gonorrhoeae ◽

Antibiotic Susceptibility ◽

Culture Collection ◽

Whole Genome ◽

Genome Sequences ◽

Content Type ◽

Associated Data

ABSTRACT A culture collection of 50 Neisseria gonorrhoeae isolates is available from the CDC & FDA Antibiotic Resistance Isolate Bank. Associated data include antibiotic susceptibility information for azithromycin, cefixime, cefpodoxime, ceftriaxone, tetracycline, ciprofloxacin, penicillin, and spectinomycin and linked whole-genome sequences.

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Antimicrobial Resistance of Neisseria gonorrhoeae Isolates from High-Risk Men in Johannesburg, South Africa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00906-20 ◽

2020 ◽

Vol 64 (11) ◽

Cited By ~ 1

Author(s):

Liteboho D. Maduna ◽

Marleen M. Kock ◽

Brian M. J. W. van der Veer ◽

Oscar Radebe ◽

James McIntyre ◽

...

Keyword(s):

South Africa ◽

High Risk ◽

Antimicrobial Resistance ◽

Neisseria Gonorrhoeae ◽

Genetic Relatedness ◽

Scale Up ◽

Sub Saharan Africa ◽

Molecular Testing ◽

Content Type ◽

Urethral Discharge

ABSTRACT Neisseria gonorrhoeae antimicrobial drug resistance has emerged worldwide; however, the situation in sub-Saharan Africa is not well documented. We investigated the molecular epidemiology and occurrence of antimicrobial resistance in Neisseria gonorrhoeae infections in two core transmission groups of men in Johannesburg, South Africa. We recruited men who have sex with men (MSM) presenting with urethral discharge and men with recurrent episodes of urethral discharge. Molecular testing and culture for N. gonorrhoeae were performed, followed by antimicrobial susceptibility testing. Whole-genome sequencing (WGS) was used to identify resistance-conferring mutations and to determine the genetic relatedness of the isolates. In all, 51 men were recruited; 42 (82%) had N. gonorrhoeae infections. Most gonococcal isolates were resistant to ciprofloxacin (78%) and tetracycline (74%); 33% were penicillin resistant. All gonococcal isolates were susceptible to cephalosporins and spectinomycin. Azithromycin resistance was observed in 4 (15%) isolates (epidemiological cutoff), all with mutations in the mtrR promoter region. Most of the isolates (19/27) harbored the gonococcal genetic island, which is associated with antimicrobial resistance. WGS revealed a diverse epidemic with mostly novel NG-STAR (70%) and NG-MAST (70%) sequence types. Thus, we demonstrate a high prevalence of antimicrobial resistance in Neisseria gonorrhoeae strains obtained from high-risk men in South Africa. The introduction of diagnostics and scale-up of surveillance are warranted to prevent the emergence of multidrug-resistant infections.

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Closed Genome Sequences of Three Salmonella enterica Strains Belonging to Serovars Saintpaul, Weltevreden, and Thompson, Isolated from Mexico

Microbiology Resource Announcements ◽

10.1128/mra.00656-19 ◽

2019 ◽

Vol 8 (28) ◽

Cited By ~ 2

Author(s):

Narjol Gonzalez-Escalona ◽

J. R. Aguirre-Sánchez ◽

J. R. Ibarra-Rodríguez ◽

C. Chaidez-Quiroz ◽

Jaime Martinez-Urtaza

Keyword(s):

River Water ◽

Salmonella Enterica ◽

Genome Sequences ◽

Short Read ◽

Content Type ◽

Short Read Sequencing ◽

Long Read ◽

Sequence Types

Here, we report the genome sequences of three Salmonella enterica strains belonging to serovars Weltevreden (CFSAN047349), Saintpaul (CFSAN047351), and Thompson (CFSAN047352), isolated from river water in Sinaloa, Mexico. The genomes were closed by a combination of long-read and short-read sequencing. The strain sequence types (STs) are ST365, ST50, and ST26, respectively.

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